See details for description.
show_sig_bootstrap_exposure(
bt_result,
sample = NULL,
signatures = NULL,
methods = "QP",
plot_fun = c("boxplot", "violin"),
agg_fun = c("mean", "median", "min", "max"),
highlight = "auto",
highlight_size = 4,
palette = "aaas",
title = NULL,
xlab = FALSE,
ylab = "Signature exposure",
width = 0.3,
dodge_width = 0.8,
outlier.shape = NA,
add = "jitter",
add.params = list(alpha = 0.3),
...
)
show_sig_bootstrap_error(
bt_result,
sample = NULL,
methods = "QP",
plot_fun = c("boxplot", "violin"),
agg_fun = c("mean", "median"),
highlight = "auto",
highlight_size = 4,
palette = "aaas",
title = NULL,
xlab = FALSE,
ylab = "Reconstruction error (L2 norm)",
width = 0.3,
dodge_width = 0.8,
outlier.shape = NA,
add = "jitter",
add.params = list(alpha = 0.3),
legend = "none",
...
)
show_sig_bootstrap_stability(
bt_result,
signatures = NULL,
measure = c("RMSE", "CV", "MAE", "AbsDiff"),
methods = "QP",
plot_fun = c("boxplot", "violin"),
palette = "aaas",
title = NULL,
xlab = FALSE,
ylab = "Signature instability",
width = 0.3,
outlier.shape = NA,
add = "jitter",
add.params = list(alpha = 0.3),
...
)Arguments
- bt_result
result object from sig_fit_bootstrap_batch.
- sample
a sample id.
- signatures
signatures to show.
- methods
a subset of
c("NNLS", "QP", "SA").- plot_fun
set the plot function.
- agg_fun
set the aggregation function when
sampleisNULL.- highlight
set the color for optimal solution. Default is "auto", which use the same color as bootstrap results, you can set it to color like "red", "gold", etc.
- highlight_size
size for highlighting triangle, default is
4.- palette
the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".
- title
plot main title.
- xlab
character vector specifying x axis labels. Use xlab = FALSE to hide xlab.
- ylab
character vector specifying y axis labels. Use ylab = FALSE to hide ylab.
- width
numeric value between 0 and 1 specifying box width.
- dodge_width
dodge width.
- outlier.shape
point shape of outlier. Default is 19. To hide outlier, specify
outlier.shape = NA. When jitter is added, then outliers will be automatically hidden.- add
character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see ?desc_statby for more details.
- add.params
parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").
- ...
other parameters passing to ggpubr::ggboxplot or ggpubr::ggviolin.
- legend
character specifying legend position. Allowed values are one of c("top", "bottom", "left", "right", "none"). To remove the legend use legend = "none". Legend position can be also specified using a numeric vector c(x, y); see details section.
- measure
measure to estimate the exposure instability, can be one of 'RMSE', 'CV', 'MAE' and 'AbsDiff'.
Value
a ggplot object
Details
Functions:
show_sig_bootstrap_exposure - this function plots exposures from bootstrap samples with both dotted boxplot. The optimal exposure (the exposure from original input) is shown as triangle point. Only one sample can be plotted.
show_sig_bootstrap_error - this function plots decomposition errors from bootstrap samples with both dotted boxplot. The error from optimal solution (the decomposition error from original input) is shown as triangle point. Only one sample can be plotted.
show_sig_bootstrap_stability - this function plots the signature exposure instability for specified signatures. Currently, the instability measure supports 3 types:
'RMSE' for Mean Root Squared Error (default) of bootstrap exposures and original exposures for each sample.
'CV' for Coefficient of Variation (CV) based on RMSE (i.e.
RMSE / btExposure_mean).'MAE' for Mean Absolute Error of bootstrap exposures and original exposures for each sample.
'AbsDiff' for Absolute Difference between mean bootstram exposure and original exposure.
References
Huang X, Wojtowicz D, Przytycka TM. Detecting presence of mutational signatures in cancer with confidence. Bioinformatics. 2018;34(2):330–337. doi:10.1093/bioinformatics/btx604
See also
Examples
# \donttest{
if (require("BSgenome.Hsapiens.UCSC.hg19")) {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read_maf(maf = laml.maf)
mt_tally <- sig_tally(
laml,
ref_genome = "BSgenome.Hsapiens.UCSC.hg19",
use_syn = TRUE
)
library(NMF)
mt_sig <- sig_extract(mt_tally$nmf_matrix,
n_sig = 3,
nrun = 2,
cores = 1
)
mat <- t(mt_tally$nmf_matrix)
mat <- mat[, colSums(mat) > 0]
bt_result <- sig_fit_bootstrap_batch(mat, sig = mt_sig, n = 10)
## Parallel computation
## bt_result = sig_fit_bootstrap_batch(mat, sig = mt_sig, n = 10, use_parallel = TRUE)
## At default, mean bootstrap exposure for each sample has been calculated
p <- show_sig_bootstrap_exposure(bt_result, methods = c("QP"))
## Show bootstrap exposure (optimal exposure is shown as triangle)
p1 <- show_sig_bootstrap_exposure(bt_result, methods = c("QP"), sample = "TCGA-AB-2802")
p1
p2 <- show_sig_bootstrap_exposure(bt_result,
methods = c("QP"),
sample = "TCGA-AB-3012",
signatures = c("Sig1", "Sig2")
)
p2
## Show bootstrap error
## Similar to exposure above
p <- show_sig_bootstrap_error(bt_result, methods = c("QP"))
p
p3 <- show_sig_bootstrap_error(bt_result, methods = c("QP"), sample = "TCGA-AB-2802")
p3
## Show exposure (in)stability
p4 <- show_sig_bootstrap_stability(bt_result, methods = c("QP"))
p4
p5 <- show_sig_bootstrap_stability(bt_result, methods = c("QP"), measure = "MAE")
p5
p6 <- show_sig_bootstrap_stability(bt_result, methods = c("QP"), measure = "AbsDiff")
p6
p7 <- show_sig_bootstrap_stability(bt_result, methods = c("QP"), measure = "CV")
p7
} else {
message("Please install package 'BSgenome.Hsapiens.UCSC.hg19' firstly!")
}
#> -Reading
#> -Validating
#> -Silent variants: 475
#> -Summarizing
#> -Processing clinical data
#> --Missing clinical data
#> -Finished in 0.161s elapsed (0.202s cpu)
#> ℹ [2024-08-04 14:40:37.664096]: Started.
#> ℹ [2024-08-04 14:40:37.668349]: We would assume you marked all variants' position in + strand.
#> ✔ [2024-08-04 14:40:37.670048]: Reference genome loaded.
#> ✔ [2024-08-04 14:40:37.674674]: Variants from MAF object queried.
#> ✔ [2024-08-04 14:40:37.677283]: Chromosome names checked.
#> ✔ [2024-08-04 14:40:37.692317]: Sex chromosomes properly handled.
#> ✔ [2024-08-04 14:40:37.695646]: Only variants located in standard chromosomes (1:22, X, Y, M/MT) are kept.
#> ✔ [2024-08-04 14:40:37.701435]: Variant start and end position checked.
#> ✔ [2024-08-04 14:40:37.705535]: Variant data for matrix generation preprocessed.
#> ℹ [2024-08-04 14:40:37.706909]: SBS matrix generation - start.
#> ℹ [2024-08-04 14:40:37.708763]: Extracting 5' and 3' adjacent bases.
#> ℹ [2024-08-04 14:40:37.991488]: Extracting +/- 20bp around mutated bases for background C>T estimation.
#> ℹ [2024-08-04 14:40:38.327775]: Estimating APOBEC enrichment scores.
#> ℹ [2024-08-04 14:40:38.329623]: Performing one-way Fisher's test for APOBEC enrichment.
#> ✔ [2024-08-04 14:40:38.402982]: APOBEC related mutations are enriched in 3.297% of samples (APOBEC enrichment score > 2; 6 of 182 samples)
#> ℹ [2024-08-04 14:40:38.406409]: Creating SBS sample-by-component matrices.
#> ✔ [2024-08-04 14:40:38.410667]: SBS-6 matrix created.
#> ✔ [2024-08-04 14:40:38.415467]: SBS-96 matrix created.
#> ✔ [2024-08-04 14:40:38.429237]: SBS-1536 matrix created.
#> ℹ [2024-08-04 14:40:38.43062]: Return SBS-96 as major matrix.
#> ✔ [2024-08-04 14:40:38.433017]: Done.
#> ℹ [2024-08-04 14:40:38.434464]: 0.77 secs elapsed.
#> The follow samples dropped due to null catalogue:
#> TCGA-AB-2823, TCGA-AB-2840, TCGA-AB-2848, TCGA-AB-2909, TCGA-AB-2942
#> NMF algorithm: 'brunet'
#> Multiple runs: 2
#> Mode: sequential [foreach:doParallelMC]
#>
Runs: |
Runs: | | 0%
Runs: |
Runs: |================= | 33%
Runs: |
Runs: |================================= | 67%
Runs: |
Runs: |==================================================| 100%
#> System time:
#> user system elapsed
#> 6.185 0.000 6.187
#> ℹ [2024-08-04 14:40:45.989708]: Batch Bootstrap Signature Exposure Analysis Started.
#> ℹ [2024-08-04 14:40:45.991445]: Samples to be filtered out: TCGA-AB-2825,TCGA-AB-2834,TCGA-AB-2866,TCGA-AB-2873,TCGA-AB-2880,TCGA-AB-2883,TCGA-AB-2892,TCGA-AB-2896,TCGA-AB-2903,TCGA-AB-2918,TCGA-AB-2933,TCGA-AB-2948,TCGA-AB-2954
#> ℹ [2024-08-04 14:40:45.992805]: Finding optimal exposures (&errors) for different methods.
#> ℹ [2024-08-04 14:40:45.994143]: Calling method `QP`.
#> ℹ [2024-08-04 14:40:45.997268]: Started.
#> ℹ [2024-08-04 14:40:45.998574]: Signature index not detected.
#> ✔ [2024-08-04 14:40:45.999875]: Signature object detected.
#> ✔ [2024-08-04 14:40:46.001174]: Database and index checked.
#> ✔ [2024-08-04 14:40:46.002604]: Signature normalized.
#> ℹ [2024-08-04 14:40:46.0039]: Checking row number for catalog matrix and signature matrix.
#> ✔ [2024-08-04 14:40:46.005178]: Checked.
#> ℹ [2024-08-04 14:40:46.006471]: Checking rownames for catalog matrix and signature matrix.
#> ✔ [2024-08-04 14:40:46.007753]: Checked.
#> ✔ [2024-08-04 14:40:46.009022]: Method 'QP' detected.
#> ✔ [2024-08-04 14:40:46.010336]: Corresponding function generated.
#> ℹ [2024-08-04 14:40:46.011604]: Calling function.
#> ℹ [2024-08-04 14:40:46.013689]: Fitting sample: TCGA-AB-2802
#> ℹ [2024-08-04 14:40:46.015093]: Fitting sample: TCGA-AB-2803
#> ℹ [2024-08-04 14:40:46.016452]: Fitting sample: TCGA-AB-2804
#> ℹ [2024-08-04 14:40:46.017856]: Fitting sample: TCGA-AB-2805
#> ℹ [2024-08-04 14:40:46.019209]: Fitting sample: TCGA-AB-2806
#> ℹ [2024-08-04 14:40:46.020559]: Fitting sample: TCGA-AB-2807
#> ℹ [2024-08-04 14:40:46.021929]: Fitting sample: TCGA-AB-2808
#> ℹ [2024-08-04 14:40:46.02327]: Fitting sample: TCGA-AB-2809
#> ℹ [2024-08-04 14:40:46.024612]: Fitting sample: TCGA-AB-2810
#> ℹ [2024-08-04 14:40:46.025978]: Fitting sample: TCGA-AB-2812
#> ℹ [2024-08-04 14:40:46.027311]: Fitting sample: TCGA-AB-2813
#> ℹ [2024-08-04 14:40:46.028644]: Fitting sample: TCGA-AB-2814
#> ℹ [2024-08-04 14:40:46.030018]: Fitting sample: TCGA-AB-2816
#> ℹ [2024-08-04 14:40:46.031354]: Fitting sample: TCGA-AB-2817
#> ℹ [2024-08-04 14:40:46.03269]: Fitting sample: TCGA-AB-2818
#> ℹ [2024-08-04 14:40:46.03408]: Fitting sample: TCGA-AB-2819
#> ℹ [2024-08-04 14:40:46.035418]: Fitting sample: TCGA-AB-2820
#> ℹ [2024-08-04 14:40:46.036763]: Fitting sample: TCGA-AB-2821
#> ℹ [2024-08-04 14:40:46.038131]: Fitting sample: TCGA-AB-2822
#> ℹ [2024-08-04 14:40:46.039468]: Fitting sample: TCGA-AB-2824
#> ℹ [2024-08-04 14:40:46.040841]: Fitting sample: TCGA-AB-2826
#> ℹ [2024-08-04 14:40:46.04228]: Fitting sample: TCGA-AB-2827
#> ℹ [2024-08-04 14:40:46.043633]: Fitting sample: TCGA-AB-2828
#> ℹ [2024-08-04 14:40:46.044979]: Fitting sample: TCGA-AB-2829
#> ℹ [2024-08-04 14:40:46.046356]: Fitting sample: TCGA-AB-2830
#> ℹ [2024-08-04 14:40:46.047709]: Fitting sample: TCGA-AB-2831
#> ℹ [2024-08-04 14:40:46.049051]: Fitting sample: TCGA-AB-2832
#> ℹ [2024-08-04 14:40:46.050418]: Fitting sample: TCGA-AB-2833
#> ℹ [2024-08-04 14:40:46.051771]: Fitting sample: TCGA-AB-2835
#> ℹ [2024-08-04 14:40:46.053109]: Fitting sample: TCGA-AB-2836
#> ℹ [2024-08-04 14:40:46.054481]: Fitting sample: TCGA-AB-2838
#> ℹ [2024-08-04 14:40:46.055827]: Fitting sample: TCGA-AB-2839
#> ℹ [2024-08-04 14:40:46.057165]: Fitting sample: TCGA-AB-2841
#> ℹ [2024-08-04 14:40:46.058532]: Fitting sample: TCGA-AB-2842
#> ℹ [2024-08-04 14:40:46.059872]: Fitting sample: TCGA-AB-2843
#> ℹ [2024-08-04 14:40:46.061208]: Fitting sample: TCGA-AB-2844
#> ℹ [2024-08-04 14:40:46.062568]: Fitting sample: TCGA-AB-2845
#> ℹ [2024-08-04 14:40:46.063899]: Fitting sample: TCGA-AB-2846
#> ℹ [2024-08-04 14:40:46.06526]: Fitting sample: TCGA-AB-2847
#> ℹ [2024-08-04 14:40:46.066616]: Fitting sample: TCGA-AB-2849
#> ℹ [2024-08-04 14:40:46.067954]: Fitting sample: TCGA-AB-2850
#> ℹ [2024-08-04 14:40:46.069331]: Fitting sample: TCGA-AB-2851
#> ℹ [2024-08-04 14:40:46.07067]: Fitting sample: TCGA-AB-2853
#> ℹ [2024-08-04 14:40:46.072002]: Fitting sample: TCGA-AB-2854
#> ℹ [2024-08-04 14:40:46.073394]: Fitting sample: TCGA-AB-2855
#> ℹ [2024-08-04 14:40:46.074733]: Fitting sample: TCGA-AB-2857
#> ℹ [2024-08-04 14:40:46.076111]: Fitting sample: TCGA-AB-2858
#> ℹ [2024-08-04 14:40:46.077493]: Fitting sample: TCGA-AB-2859
#> ℹ [2024-08-04 14:40:46.078837]: Fitting sample: TCGA-AB-2860
#> ℹ [2024-08-04 14:40:46.080181]: Fitting sample: TCGA-AB-2861
#> ℹ [2024-08-04 14:40:46.081554]: Fitting sample: TCGA-AB-2862
#> ℹ [2024-08-04 14:40:46.082899]: Fitting sample: TCGA-AB-2863
#> ℹ [2024-08-04 14:40:46.084255]: Fitting sample: TCGA-AB-2864
#> ℹ [2024-08-04 14:40:46.08562]: Fitting sample: TCGA-AB-2865
#> ℹ [2024-08-04 14:40:46.087002]: Fitting sample: TCGA-AB-2867
#> ℹ [2024-08-04 14:40:46.088347]: Fitting sample: TCGA-AB-2868
#> ℹ [2024-08-04 14:40:46.089714]: Fitting sample: TCGA-AB-2869
#> ℹ [2024-08-04 14:40:46.091053]: Fitting sample: TCGA-AB-2870
#> ℹ [2024-08-04 14:40:46.092388]: Fitting sample: TCGA-AB-2871
#> ℹ [2024-08-04 14:40:46.093776]: Fitting sample: TCGA-AB-2872
#> ℹ [2024-08-04 14:40:46.095119]: Fitting sample: TCGA-AB-2874
#> ℹ [2024-08-04 14:40:46.096468]: Fitting sample: TCGA-AB-2875
#> ℹ [2024-08-04 14:40:46.09789]: Fitting sample: TCGA-AB-2876
#> ℹ [2024-08-04 14:40:46.099246]: Fitting sample: TCGA-AB-2877
#> ℹ [2024-08-04 14:40:46.100598]: Fitting sample: TCGA-AB-2878
#> ℹ [2024-08-04 14:40:46.101978]: Fitting sample: TCGA-AB-2879
#> ℹ [2024-08-04 14:40:46.103324]: Fitting sample: TCGA-AB-2881
#> ℹ [2024-08-04 14:40:46.104666]: Fitting sample: TCGA-AB-2882
#> ℹ [2024-08-04 14:40:46.106058]: Fitting sample: TCGA-AB-2884
#> ℹ [2024-08-04 14:40:46.107411]: Fitting sample: TCGA-AB-2885
#> ℹ [2024-08-04 14:40:46.108751]: Fitting sample: TCGA-AB-2886
#> ℹ [2024-08-04 14:40:46.11012]: Fitting sample: TCGA-AB-2887
#> ℹ [2024-08-04 14:40:46.11146]: Fitting sample: TCGA-AB-2888
#> ℹ [2024-08-04 14:40:46.112798]: Fitting sample: TCGA-AB-2889
#> ℹ [2024-08-04 14:40:46.114157]: Fitting sample: TCGA-AB-2890
#> ℹ [2024-08-04 14:40:46.115491]: Fitting sample: TCGA-AB-2891
#> ℹ [2024-08-04 14:40:46.116838]: Fitting sample: TCGA-AB-2894
#> ℹ [2024-08-04 14:40:46.1182]: Fitting sample: TCGA-AB-2895
#> ℹ [2024-08-04 14:40:46.11953]: Fitting sample: TCGA-AB-2897
#> ℹ [2024-08-04 14:40:46.120868]: Fitting sample: TCGA-AB-2898
#> ℹ [2024-08-04 14:40:46.122232]: Fitting sample: TCGA-AB-2899
#> ℹ [2024-08-04 14:40:46.123573]: Fitting sample: TCGA-AB-2900
#> ℹ [2024-08-04 14:40:46.124903]: Fitting sample: TCGA-AB-2901
#> ℹ [2024-08-04 14:40:46.126272]: Fitting sample: TCGA-AB-2904
#> ℹ [2024-08-04 14:40:46.127609]: Fitting sample: TCGA-AB-2905
#> ℹ [2024-08-04 14:40:46.128943]: Fitting sample: TCGA-AB-2906
#> ℹ [2024-08-04 14:40:46.130314]: Fitting sample: TCGA-AB-2907
#> ℹ [2024-08-04 14:40:46.131662]: Fitting sample: TCGA-AB-2908
#> ℹ [2024-08-04 14:40:46.133019]: Fitting sample: TCGA-AB-2910
#> ℹ [2024-08-04 14:40:46.134376]: Fitting sample: TCGA-AB-2911
#> ℹ [2024-08-04 14:40:46.135708]: Fitting sample: TCGA-AB-2912
#> ℹ [2024-08-04 14:40:46.137044]: Fitting sample: TCGA-AB-2913
#> ℹ [2024-08-04 14:40:46.138397]: Fitting sample: TCGA-AB-2914
#> ℹ [2024-08-04 14:40:46.139732]: Fitting sample: TCGA-AB-2915
#> ℹ [2024-08-04 14:40:46.141075]: Fitting sample: TCGA-AB-2916
#> ℹ [2024-08-04 14:40:46.14247]: Fitting sample: TCGA-AB-2917
#> ℹ [2024-08-04 14:40:46.143828]: Fitting sample: TCGA-AB-2919
#> ℹ [2024-08-04 14:40:46.145174]: Fitting sample: TCGA-AB-2920
#> ℹ [2024-08-04 14:40:46.146653]: Fitting sample: TCGA-AB-2921
#> ℹ [2024-08-04 14:40:46.148026]: Fitting sample: TCGA-AB-2922
#> ℹ [2024-08-04 14:40:46.149385]: Fitting sample: TCGA-AB-2923
#> ℹ [2024-08-04 14:40:46.15073]: Fitting sample: TCGA-AB-2924
#> ℹ [2024-08-04 14:40:46.152066]: Fitting sample: TCGA-AB-2925
#> ℹ [2024-08-04 14:40:46.153447]: Fitting sample: TCGA-AB-2926
#> ℹ [2024-08-04 14:40:46.154854]: Fitting sample: TCGA-AB-2927
#> ℹ [2024-08-04 14:40:46.156212]: Fitting sample: TCGA-AB-2928
#> ℹ [2024-08-04 14:40:46.157573]: Fitting sample: TCGA-AB-2929
#> ℹ [2024-08-04 14:40:46.158909]: Fitting sample: TCGA-AB-2930
#> ℹ [2024-08-04 14:40:46.160241]: Fitting sample: TCGA-AB-2931
#> ℹ [2024-08-04 14:40:46.1616]: Fitting sample: TCGA-AB-2932
#> ℹ [2024-08-04 14:40:46.162943]: Fitting sample: TCGA-AB-2934
#> ℹ [2024-08-04 14:40:46.164275]: Fitting sample: TCGA-AB-2935
#> ℹ [2024-08-04 14:40:46.165631]: Fitting sample: TCGA-AB-2936
#> ℹ [2024-08-04 14:40:46.166978]: Fitting sample: TCGA-AB-2937
#> ℹ [2024-08-04 14:40:46.168313]: Fitting sample: TCGA-AB-2938
#> ℹ [2024-08-04 14:40:46.169672]: Fitting sample: TCGA-AB-2939
#> ℹ [2024-08-04 14:40:46.171001]: Fitting sample: TCGA-AB-2940
#> ℹ [2024-08-04 14:40:46.172342]: Fitting sample: TCGA-AB-2941
#> ℹ [2024-08-04 14:40:46.173712]: Fitting sample: TCGA-AB-2943
#> ℹ [2024-08-04 14:40:46.175062]: Fitting sample: TCGA-AB-2945
#> ℹ [2024-08-04 14:40:46.176404]: Fitting sample: TCGA-AB-2946
#> ℹ [2024-08-04 14:40:46.177801]: Fitting sample: TCGA-AB-2947
#> ℹ [2024-08-04 14:40:46.179158]: Fitting sample: TCGA-AB-2949
#> ℹ [2024-08-04 14:40:46.18049]: Fitting sample: TCGA-AB-2950
#> ℹ [2024-08-04 14:40:46.181888]: Fitting sample: TCGA-AB-2952
#> ℹ [2024-08-04 14:40:46.183233]: Fitting sample: TCGA-AB-2955
#> ℹ [2024-08-04 14:40:46.192791]: Fitting sample: TCGA-AB-2956
#> ℹ [2024-08-04 14:40:46.194577]: Fitting sample: TCGA-AB-2957
#> ℹ [2024-08-04 14:40:46.19596]: Fitting sample: TCGA-AB-2959
#> ℹ [2024-08-04 14:40:46.19737]: Fitting sample: TCGA-AB-2963
#> ℹ [2024-08-04 14:40:46.198722]: Fitting sample: TCGA-AB-2964
#> ℹ [2024-08-04 14:40:46.200068]: Fitting sample: TCGA-AB-2965
#> ℹ [2024-08-04 14:40:46.201442]: Fitting sample: TCGA-AB-2966
#> ℹ [2024-08-04 14:40:46.202899]: Fitting sample: TCGA-AB-2967
#> ℹ [2024-08-04 14:40:46.204257]: Fitting sample: TCGA-AB-2968
#> ℹ [2024-08-04 14:40:46.205634]: Fitting sample: TCGA-AB-2970
#> ℹ [2024-08-04 14:40:46.206977]: Fitting sample: TCGA-AB-2971
#> ℹ [2024-08-04 14:40:46.208323]: Fitting sample: TCGA-AB-2972
#> ℹ [2024-08-04 14:40:46.209684]: Fitting sample: TCGA-AB-2973
#> ℹ [2024-08-04 14:40:46.211038]: Fitting sample: TCGA-AB-2974
#> ℹ [2024-08-04 14:40:46.212367]: Fitting sample: TCGA-AB-2975
#> ℹ [2024-08-04 14:40:46.213748]: Fitting sample: TCGA-AB-2976
#> ℹ [2024-08-04 14:40:46.215095]: Fitting sample: TCGA-AB-2977
#> ℹ [2024-08-04 14:40:46.216443]: Fitting sample: TCGA-AB-2978
#> ℹ [2024-08-04 14:40:46.217805]: Fitting sample: TCGA-AB-2979
#> ℹ [2024-08-04 14:40:46.219144]: Fitting sample: TCGA-AB-2980
#> ℹ [2024-08-04 14:40:46.220492]: Fitting sample: TCGA-AB-2981
#> ℹ [2024-08-04 14:40:46.221869]: Fitting sample: TCGA-AB-2982
#> ℹ [2024-08-04 14:40:46.223207]: Fitting sample: TCGA-AB-2983
#> ℹ [2024-08-04 14:40:46.224551]: Fitting sample: TCGA-AB-2984
#> ℹ [2024-08-04 14:40:46.225929]: Fitting sample: TCGA-AB-2985
#> ℹ [2024-08-04 14:40:46.22727]: Fitting sample: TCGA-AB-2986
#> ℹ [2024-08-04 14:40:46.228604]: Fitting sample: TCGA-AB-2987
#> ℹ [2024-08-04 14:40:46.229961]: Fitting sample: TCGA-AB-2988
#> ℹ [2024-08-04 14:40:46.231295]: Fitting sample: TCGA-AB-2989
#> ℹ [2024-08-04 14:40:46.232641]: Fitting sample: TCGA-AB-2990
#> ℹ [2024-08-04 14:40:46.234032]: Fitting sample: TCGA-AB-2991
#> ℹ [2024-08-04 14:40:46.235379]: Fitting sample: TCGA-AB-2992
#> ℹ [2024-08-04 14:40:46.236744]: Fitting sample: TCGA-AB-2993
#> ℹ [2024-08-04 14:40:46.238128]: Fitting sample: TCGA-AB-2994
#> ℹ [2024-08-04 14:40:46.239465]: Fitting sample: TCGA-AB-2995
#> ℹ [2024-08-04 14:40:46.2408]: Fitting sample: TCGA-AB-2996
#> ℹ [2024-08-04 14:40:46.242223]: Fitting sample: TCGA-AB-2997
#> ℹ [2024-08-04 14:40:46.24357]: Fitting sample: TCGA-AB-2998
#> ℹ [2024-08-04 14:40:46.244956]: Fitting sample: TCGA-AB-2999
#> ℹ [2024-08-04 14:40:46.246344]: Fitting sample: TCGA-AB-3000
#> ℹ [2024-08-04 14:40:46.247683]: Fitting sample: TCGA-AB-3001
#> ℹ [2024-08-04 14:40:46.249042]: Fitting sample: TCGA-AB-3002
#> ℹ [2024-08-04 14:40:46.250414]: Fitting sample: TCGA-AB-3005
#> ℹ [2024-08-04 14:40:46.251752]: Fitting sample: TCGA-AB-3006
#> ℹ [2024-08-04 14:40:46.25309]: Fitting sample: TCGA-AB-3007
#> ℹ [2024-08-04 14:40:46.254461]: Fitting sample: TCGA-AB-3008
#> ℹ [2024-08-04 14:40:46.25581]: Fitting sample: TCGA-AB-3009
#> ℹ [2024-08-04 14:40:46.257181]: Fitting sample: TCGA-AB-3011
#> ℹ [2024-08-04 14:40:46.258545]: Fitting sample: TCGA-AB-3012
#> ✔ [2024-08-04 14:40:46.259889]: Done.
#> ℹ [2024-08-04 14:40:46.261172]: Generating output signature exposures.
#> ✔ [2024-08-04 14:40:46.273708]: Done.
#> ℹ [2024-08-04 14:40:46.275057]: Calculating errors (Frobenius Norm).
#> ✔ [2024-08-04 14:40:46.320648]: Done.
#> ℹ [2024-08-04 14:40:46.322095]: 0.325 secs elapsed.
#> ℹ [2024-08-04 14:40:46.325051]: Getting bootstrap exposures (&errors/similarity) for different methods.
#> ℹ [2024-08-04 14:40:46.326409]: This step is time consuming, please be patient.
#> ℹ [2024-08-04 14:40:46.328268]: Processing sample `TCGA-AB-2802`.
#> ℹ [2024-08-04 14:40:47.356703]: Processing sample `TCGA-AB-2803`.
#> ℹ [2024-08-04 14:40:48.376168]: Processing sample `TCGA-AB-2804`.
#> ℹ [2024-08-04 14:40:49.395839]: Processing sample `TCGA-AB-2805`.
#> ℹ [2024-08-04 14:40:50.416847]: Processing sample `TCGA-AB-2806`.
#> ℹ [2024-08-04 14:40:51.43472]: Processing sample `TCGA-AB-2807`.
#> ℹ [2024-08-04 14:40:52.457253]: Processing sample `TCGA-AB-2808`.
#> ℹ [2024-08-04 14:40:53.477395]: Processing sample `TCGA-AB-2809`.
#> ℹ [2024-08-04 14:40:54.494114]: Processing sample `TCGA-AB-2810`.
#> ℹ [2024-08-04 14:40:55.511731]: Processing sample `TCGA-AB-2812`.
#> ℹ [2024-08-04 14:40:56.533058]: Processing sample `TCGA-AB-2813`.
#> ℹ [2024-08-04 14:40:57.55427]: Processing sample `TCGA-AB-2814`.
#> ℹ [2024-08-04 14:40:58.576124]: Processing sample `TCGA-AB-2816`.
#> ℹ [2024-08-04 14:40:59.598608]: Processing sample `TCGA-AB-2817`.
#> ℹ [2024-08-04 14:41:00.618478]: Processing sample `TCGA-AB-2818`.
#> ℹ [2024-08-04 14:41:01.638554]: Processing sample `TCGA-AB-2819`.
#> ℹ [2024-08-04 14:41:02.659537]: Processing sample `TCGA-AB-2820`.
#> ℹ [2024-08-04 14:41:03.67956]: Processing sample `TCGA-AB-2821`.
#> ℹ [2024-08-04 14:41:04.700149]: Processing sample `TCGA-AB-2822`.
#> ℹ [2024-08-04 14:41:05.718509]: Processing sample `TCGA-AB-2824`.
#> ℹ [2024-08-04 14:41:06.743135]: Processing sample `TCGA-AB-2826`.
#> ℹ [2024-08-04 14:41:07.764142]: Processing sample `TCGA-AB-2827`.
#> ℹ [2024-08-04 14:41:08.783917]: Processing sample `TCGA-AB-2828`.
#> ℹ [2024-08-04 14:41:09.801319]: Processing sample `TCGA-AB-2829`.
#> ℹ [2024-08-04 14:41:10.884157]: Processing sample `TCGA-AB-2830`.
#> ℹ [2024-08-04 14:41:11.916865]: Processing sample `TCGA-AB-2831`.
#> ℹ [2024-08-04 14:41:12.94477]: Processing sample `TCGA-AB-2832`.
#> ℹ [2024-08-04 14:41:13.966254]: Processing sample `TCGA-AB-2833`.
#> ℹ [2024-08-04 14:41:14.987149]: Processing sample `TCGA-AB-2835`.
#> ℹ [2024-08-04 14:41:16.007392]: Processing sample `TCGA-AB-2836`.
#> ℹ [2024-08-04 14:41:17.031114]: Processing sample `TCGA-AB-2838`.
#> ℹ [2024-08-04 14:41:18.04649]: Processing sample `TCGA-AB-2839`.
#> ℹ [2024-08-04 14:41:19.062923]: Processing sample `TCGA-AB-2841`.
#> ℹ [2024-08-04 14:41:20.081197]: Processing sample `TCGA-AB-2842`.
#> ℹ [2024-08-04 14:41:21.099023]: Processing sample `TCGA-AB-2843`.
#> ℹ [2024-08-04 14:41:22.11705]: Processing sample `TCGA-AB-2844`.
#> ℹ [2024-08-04 14:41:23.144931]: Processing sample `TCGA-AB-2845`.
#> ℹ [2024-08-04 14:41:24.174626]: Processing sample `TCGA-AB-2846`.
#> ℹ [2024-08-04 14:41:25.197912]: Processing sample `TCGA-AB-2847`.
#> ℹ [2024-08-04 14:41:26.22601]: Processing sample `TCGA-AB-2849`.
#> ℹ [2024-08-04 14:41:27.252748]: Processing sample `TCGA-AB-2850`.
#> ℹ [2024-08-04 14:41:28.278752]: Processing sample `TCGA-AB-2851`.
#> ℹ [2024-08-04 14:41:29.302976]: Processing sample `TCGA-AB-2853`.
#> ℹ [2024-08-04 14:41:30.327061]: Processing sample `TCGA-AB-2854`.
#> ℹ [2024-08-04 14:41:31.349844]: Processing sample `TCGA-AB-2855`.
#> ℹ [2024-08-04 14:41:32.377017]: Processing sample `TCGA-AB-2857`.
#> ℹ [2024-08-04 14:41:33.398252]: Processing sample `TCGA-AB-2858`.
#> ℹ [2024-08-04 14:41:34.419698]: Processing sample `TCGA-AB-2859`.
#> ℹ [2024-08-04 14:41:35.440498]: Processing sample `TCGA-AB-2860`.
#> ℹ [2024-08-04 14:41:36.461965]: Processing sample `TCGA-AB-2861`.
#> ℹ [2024-08-04 14:41:37.484421]: Processing sample `TCGA-AB-2862`.
#> ℹ [2024-08-04 14:41:38.506494]: Processing sample `TCGA-AB-2863`.
#> ℹ [2024-08-04 14:41:39.524838]: Processing sample `TCGA-AB-2864`.
#> ℹ [2024-08-04 14:41:40.541017]: Processing sample `TCGA-AB-2865`.
#> ℹ [2024-08-04 14:41:41.566596]: Processing sample `TCGA-AB-2867`.
#> ℹ [2024-08-04 14:41:42.597193]: Processing sample `TCGA-AB-2868`.
#> ℹ [2024-08-04 14:41:43.623842]: Processing sample `TCGA-AB-2869`.
#> ℹ [2024-08-04 14:41:44.673694]: Processing sample `TCGA-AB-2870`.
#> ℹ [2024-08-04 14:41:45.698563]: Processing sample `TCGA-AB-2871`.
#> ℹ [2024-08-04 14:41:46.741868]: Processing sample `TCGA-AB-2872`.
#> ℹ [2024-08-04 14:41:47.773419]: Processing sample `TCGA-AB-2874`.
#> ℹ [2024-08-04 14:41:48.793688]: Processing sample `TCGA-AB-2875`.
#> ℹ [2024-08-04 14:41:49.80757]: Processing sample `TCGA-AB-2876`.
#> ℹ [2024-08-04 14:41:50.820921]: Processing sample `TCGA-AB-2877`.
#> ℹ [2024-08-04 14:41:51.837371]: Processing sample `TCGA-AB-2878`.
#> ℹ [2024-08-04 14:41:52.889159]: Processing sample `TCGA-AB-2879`.
#> ℹ [2024-08-04 14:41:53.904878]: Processing sample `TCGA-AB-2881`.
#> ℹ [2024-08-04 14:41:54.918548]: Processing sample `TCGA-AB-2882`.
#> ℹ [2024-08-04 14:41:55.931516]: Processing sample `TCGA-AB-2884`.
#> ℹ [2024-08-04 14:41:56.94437]: Processing sample `TCGA-AB-2885`.
#> ℹ [2024-08-04 14:41:57.979967]: Processing sample `TCGA-AB-2886`.
#> ℹ [2024-08-04 14:41:59.002915]: Processing sample `TCGA-AB-2887`.
#> ℹ [2024-08-04 14:42:00.034472]: Processing sample `TCGA-AB-2888`.
#> ℹ [2024-08-04 14:42:01.055183]: Processing sample `TCGA-AB-2889`.
#> ℹ [2024-08-04 14:42:02.089924]: Processing sample `TCGA-AB-2890`.
#> ℹ [2024-08-04 14:42:03.11572]: Processing sample `TCGA-AB-2891`.
#> ℹ [2024-08-04 14:42:04.15028]: Processing sample `TCGA-AB-2894`.
#> ℹ [2024-08-04 14:42:05.169899]: Processing sample `TCGA-AB-2895`.
#> ℹ [2024-08-04 14:42:06.185279]: Processing sample `TCGA-AB-2897`.
#> ℹ [2024-08-04 14:42:07.204235]: Processing sample `TCGA-AB-2898`.
#> ℹ [2024-08-04 14:42:08.22186]: Processing sample `TCGA-AB-2899`.
#> ℹ [2024-08-04 14:42:09.246165]: Processing sample `TCGA-AB-2900`.
#> ℹ [2024-08-04 14:42:10.263499]: Processing sample `TCGA-AB-2901`.
#> ℹ [2024-08-04 14:42:11.281967]: Processing sample `TCGA-AB-2904`.
#> ℹ [2024-08-04 14:42:12.304629]: Processing sample `TCGA-AB-2905`.
#> ℹ [2024-08-04 14:42:13.321273]: Processing sample `TCGA-AB-2906`.
#> ℹ [2024-08-04 14:42:14.334093]: Processing sample `TCGA-AB-2907`.
#> ℹ [2024-08-04 14:42:15.350477]: Processing sample `TCGA-AB-2908`.
#> ℹ [2024-08-04 14:42:16.367467]: Processing sample `TCGA-AB-2910`.
#> ℹ [2024-08-04 14:42:17.378138]: Processing sample `TCGA-AB-2911`.
#> ℹ [2024-08-04 14:42:18.388766]: Processing sample `TCGA-AB-2912`.
#> ℹ [2024-08-04 14:42:19.399625]: Processing sample `TCGA-AB-2913`.
#> ℹ [2024-08-04 14:42:20.421729]: Processing sample `TCGA-AB-2914`.
#> ℹ [2024-08-04 14:42:21.437553]: Processing sample `TCGA-AB-2915`.
#> ℹ [2024-08-04 14:42:22.454155]: Processing sample `TCGA-AB-2916`.
#> ℹ [2024-08-04 14:42:23.471853]: Processing sample `TCGA-AB-2917`.
#> ℹ [2024-08-04 14:42:24.488167]: Processing sample `TCGA-AB-2919`.
#> ℹ [2024-08-04 14:42:25.499418]: Processing sample `TCGA-AB-2920`.
#> ℹ [2024-08-04 14:42:26.513835]: Processing sample `TCGA-AB-2921`.
#> ℹ [2024-08-04 14:42:27.527299]: Processing sample `TCGA-AB-2922`.
#> ℹ [2024-08-04 14:42:28.5365]: Processing sample `TCGA-AB-2923`.
#> ℹ [2024-08-04 14:42:29.550592]: Processing sample `TCGA-AB-2924`.
#> ℹ [2024-08-04 14:42:30.562055]: Processing sample `TCGA-AB-2925`.
#> ℹ [2024-08-04 14:42:31.575113]: Processing sample `TCGA-AB-2926`.
#> ℹ [2024-08-04 14:42:32.589014]: Processing sample `TCGA-AB-2927`.
#> ℹ [2024-08-04 14:42:33.601103]: Processing sample `TCGA-AB-2928`.
#> ℹ [2024-08-04 14:42:34.609095]: Processing sample `TCGA-AB-2929`.
#> ℹ [2024-08-04 14:42:35.625724]: Processing sample `TCGA-AB-2930`.
#> ℹ [2024-08-04 14:42:36.643424]: Processing sample `TCGA-AB-2931`.
#> ℹ [2024-08-04 14:42:37.657516]: Processing sample `TCGA-AB-2932`.
#> ℹ [2024-08-04 14:42:38.671598]: Processing sample `TCGA-AB-2934`.
#> ℹ [2024-08-04 14:42:39.681425]: Processing sample `TCGA-AB-2935`.
#> ℹ [2024-08-04 14:42:40.69207]: Processing sample `TCGA-AB-2936`.
#> ℹ [2024-08-04 14:42:41.700834]: Processing sample `TCGA-AB-2937`.
#> ℹ [2024-08-04 14:42:42.711565]: Processing sample `TCGA-AB-2938`.
#> ℹ [2024-08-04 14:42:43.719518]: Processing sample `TCGA-AB-2939`.
#> ℹ [2024-08-04 14:42:44.730128]: Processing sample `TCGA-AB-2940`.
#> ℹ [2024-08-04 14:42:45.739432]: Processing sample `TCGA-AB-2941`.
#> ℹ [2024-08-04 14:42:46.748186]: Processing sample `TCGA-AB-2943`.
#> ℹ [2024-08-04 14:42:47.759816]: Processing sample `TCGA-AB-2945`.
#> ℹ [2024-08-04 14:42:48.766542]: Processing sample `TCGA-AB-2946`.
#> ℹ [2024-08-04 14:42:49.774621]: Processing sample `TCGA-AB-2947`.
#> ℹ [2024-08-04 14:42:50.782102]: Processing sample `TCGA-AB-2949`.
#> ℹ [2024-08-04 14:42:51.791797]: Processing sample `TCGA-AB-2950`.
#> ℹ [2024-08-04 14:42:52.833206]: Processing sample `TCGA-AB-2952`.
#> ℹ [2024-08-04 14:42:53.843637]: Processing sample `TCGA-AB-2955`.
#> ℹ [2024-08-04 14:42:54.850744]: Processing sample `TCGA-AB-2956`.
#> ℹ [2024-08-04 14:42:55.861294]: Processing sample `TCGA-AB-2957`.
#> ℹ [2024-08-04 14:42:56.880051]: Processing sample `TCGA-AB-2959`.
#> ℹ [2024-08-04 14:42:57.889986]: Processing sample `TCGA-AB-2963`.
#> ℹ [2024-08-04 14:42:58.905467]: Processing sample `TCGA-AB-2964`.
#> ℹ [2024-08-04 14:42:59.914986]: Processing sample `TCGA-AB-2965`.
#> ℹ [2024-08-04 14:43:00.927551]: Processing sample `TCGA-AB-2966`.
#> ℹ [2024-08-04 14:43:01.946422]: Processing sample `TCGA-AB-2967`.
#> ℹ [2024-08-04 14:43:02.956758]: Processing sample `TCGA-AB-2968`.
#> ℹ [2024-08-04 14:43:03.965941]: Processing sample `TCGA-AB-2970`.
#> ℹ [2024-08-04 14:43:04.988319]: Processing sample `TCGA-AB-2971`.
#> ℹ [2024-08-04 14:43:06.007205]: Processing sample `TCGA-AB-2972`.
#> ℹ [2024-08-04 14:43:07.05766]: Processing sample `TCGA-AB-2973`.
#> ℹ [2024-08-04 14:43:08.081445]: Processing sample `TCGA-AB-2974`.
#> ℹ [2024-08-04 14:43:09.123816]: Processing sample `TCGA-AB-2975`.
#> ℹ [2024-08-04 14:43:10.285464]: Processing sample `TCGA-AB-2976`.
#> ℹ [2024-08-04 14:43:11.302745]: Processing sample `TCGA-AB-2977`.
#> ℹ [2024-08-04 14:43:12.316946]: Processing sample `TCGA-AB-2978`.
#> ℹ [2024-08-04 14:43:13.343171]: Processing sample `TCGA-AB-2979`.
#> ℹ [2024-08-04 14:43:14.359108]: Processing sample `TCGA-AB-2980`.
#> ℹ [2024-08-04 14:43:15.380588]: Processing sample `TCGA-AB-2981`.
#> ℹ [2024-08-04 14:43:16.392974]: Processing sample `TCGA-AB-2982`.
#> ℹ [2024-08-04 14:43:17.408295]: Processing sample `TCGA-AB-2983`.
#> ℹ [2024-08-04 14:43:18.429311]: Processing sample `TCGA-AB-2984`.
#> ℹ [2024-08-04 14:43:19.443393]: Processing sample `TCGA-AB-2985`.
#> ℹ [2024-08-04 14:43:20.470507]: Processing sample `TCGA-AB-2986`.
#> ℹ [2024-08-04 14:43:21.478438]: Processing sample `TCGA-AB-2987`.
#> ℹ [2024-08-04 14:43:22.499959]: Processing sample `TCGA-AB-2988`.
#> ℹ [2024-08-04 14:43:23.517951]: Processing sample `TCGA-AB-2989`.
#> ℹ [2024-08-04 14:43:24.547811]: Processing sample `TCGA-AB-2990`.
#> ℹ [2024-08-04 14:43:25.573176]: Processing sample `TCGA-AB-2991`.
#> ℹ [2024-08-04 14:43:26.635187]: Processing sample `TCGA-AB-2992`.
#> ℹ [2024-08-04 14:43:27.660817]: Processing sample `TCGA-AB-2993`.
#> ℹ [2024-08-04 14:43:28.693411]: Processing sample `TCGA-AB-2994`.
#> ℹ [2024-08-04 14:43:29.724346]: Processing sample `TCGA-AB-2995`.
#> ℹ [2024-08-04 14:43:30.748769]: Processing sample `TCGA-AB-2996`.
#> ℹ [2024-08-04 14:43:31.763514]: Processing sample `TCGA-AB-2997`.
#> ℹ [2024-08-04 14:43:32.792296]: Processing sample `TCGA-AB-2998`.
#> ℹ [2024-08-04 14:43:33.821706]: Processing sample `TCGA-AB-2999`.
#> ℹ [2024-08-04 14:43:34.835565]: Processing sample `TCGA-AB-3000`.
#> ℹ [2024-08-04 14:43:35.850063]: Processing sample `TCGA-AB-3001`.
#> ℹ [2024-08-04 14:43:36.867438]: Processing sample `TCGA-AB-3002`.
#> ℹ [2024-08-04 14:43:37.883421]: Processing sample `TCGA-AB-3005`.
#> ℹ [2024-08-04 14:43:38.899789]: Processing sample `TCGA-AB-3006`.
#> ℹ [2024-08-04 14:43:39.916936]: Processing sample `TCGA-AB-3007`.
#> ℹ [2024-08-04 14:43:40.933023]: Processing sample `TCGA-AB-3008`.
#> ℹ [2024-08-04 14:43:41.953162]: Processing sample `TCGA-AB-3009`.
#> ℹ [2024-08-04 14:43:42.972606]: Processing sample `TCGA-AB-3011`.
#> ℹ [2024-08-04 14:43:44.131154]: Processing sample `TCGA-AB-3012`.
#> ✔ [2024-08-04 14:43:45.288745]: Gotten.
#> ℹ [2024-08-04 14:43:45.291134]: Reporting p values...
#> ℹ [2024-08-04 14:43:45.292682]: Started.
#> ✔ [2024-08-04 14:43:45.294058]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.295938]: Done.
#> ℹ [2024-08-04 14:43:45.297325]: 0.005 secs elapsed.
#> ℹ [2024-08-04 14:43:45.298657]: Started.
#> ✔ [2024-08-04 14:43:45.299922]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.301599]: Done.
#> ℹ [2024-08-04 14:43:45.302922]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.304232]: Started.
#> ✔ [2024-08-04 14:43:45.305522]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.307203]: Done.
#> ℹ [2024-08-04 14:43:45.308524]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.309865]: Started.
#> ✔ [2024-08-04 14:43:45.311141]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.312807]: Done.
#> ℹ [2024-08-04 14:43:45.314195]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.315512]: Started.
#> ✔ [2024-08-04 14:43:45.316779]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.318459]: Done.
#> ℹ [2024-08-04 14:43:45.319772]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.321076]: Started.
#> ✔ [2024-08-04 14:43:45.32238]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.32404]: Done.
#> ℹ [2024-08-04 14:43:45.325384]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.326698]: Started.
#> ✔ [2024-08-04 14:43:45.327966]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.329654]: Done.
#> ℹ [2024-08-04 14:43:45.330966]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.332278]: Started.
#> ✔ [2024-08-04 14:43:45.333587]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.335253]: Done.
#> ℹ [2024-08-04 14:43:45.336572]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.337912]: Started.
#> ✔ [2024-08-04 14:43:45.339177]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.340823]: Done.
#> ℹ [2024-08-04 14:43:45.342177]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.343485]: Started.
#> ✔ [2024-08-04 14:43:45.344754]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.346441]: Done.
#> ℹ [2024-08-04 14:43:45.347774]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.349083]: Started.
#> ✔ [2024-08-04 14:43:45.350387]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.352047]: Done.
#> ℹ [2024-08-04 14:43:45.353408]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.354714]: Started.
#> ✔ [2024-08-04 14:43:45.355995]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.357667]: Done.
#> ℹ [2024-08-04 14:43:45.358994]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.360312]: Started.
#> ✔ [2024-08-04 14:43:45.361607]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.363267]: Done.
#> ℹ [2024-08-04 14:43:45.364586]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.365925]: Started.
#> ✔ [2024-08-04 14:43:45.367191]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.368856]: Done.
#> ℹ [2024-08-04 14:43:45.37024]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.371553]: Started.
#> ✔ [2024-08-04 14:43:45.37283]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.374514]: Done.
#> ℹ [2024-08-04 14:43:45.375852]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.377166]: Started.
#> ✔ [2024-08-04 14:43:45.378461]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.380135]: Done.
#> ℹ [2024-08-04 14:43:45.381476]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.382808]: Started.
#> ✔ [2024-08-04 14:43:45.384081]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.385757]: Done.
#> ℹ [2024-08-04 14:43:45.38708]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.388397]: Started.
#> ✔ [2024-08-04 14:43:45.389692]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.391366]: Done.
#> ℹ [2024-08-04 14:43:45.392688]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.394019]: Started.
#> ✔ [2024-08-04 14:43:45.395289]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.396948]: Done.
#> ℹ [2024-08-04 14:43:45.398297]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.399611]: Started.
#> ✔ [2024-08-04 14:43:45.40088]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.40258]: Done.
#> ℹ [2024-08-04 14:43:45.403896]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.405212]: Started.
#> ✔ [2024-08-04 14:43:45.406529]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.408195]: Done.
#> ℹ [2024-08-04 14:43:45.40955]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.41089]: Started.
#> ✔ [2024-08-04 14:43:45.412163]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.413852]: Done.
#> ℹ [2024-08-04 14:43:45.415164]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.416476]: Started.
#> ✔ [2024-08-04 14:43:45.41777]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.419436]: Done.
#> ℹ [2024-08-04 14:43:45.420753]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.42211]: Started.
#> ✔ [2024-08-04 14:43:45.423383]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.425039]: Done.
#> ℹ [2024-08-04 14:43:45.426382]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.427688]: Started.
#> ✔ [2024-08-04 14:43:45.42896]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.430642]: Done.
#> ℹ [2024-08-04 14:43:45.431981]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.433314]: Started.
#> ✔ [2024-08-04 14:43:45.434589]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.436252]: Done.
#> ℹ [2024-08-04 14:43:45.437599]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.438919]: Started.
#> ✔ [2024-08-04 14:43:45.440186]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.441891]: Done.
#> ℹ [2024-08-04 14:43:45.443215]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.444533]: Started.
#> ✔ [2024-08-04 14:43:45.445833]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.447531]: Done.
#> ℹ [2024-08-04 14:43:45.448881]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.45026]: Started.
#> ✔ [2024-08-04 14:43:45.451533]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.453212]: Done.
#> ℹ [2024-08-04 14:43:45.454563]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.455872]: Started.
#> ✔ [2024-08-04 14:43:45.457145]: Batch mode enabled.
#> ! [2024-08-04 14:43:45.458703]: NA result detected from t.test, reporting proportion as p value.
#> ✔ [2024-08-04 14:43:45.460216]: Done.
#> ℹ [2024-08-04 14:43:45.461582]: 0.006 secs elapsed.
#> ℹ [2024-08-04 14:43:45.462965]: Started.
#> ✔ [2024-08-04 14:43:45.464252]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.465947]: Done.
#> ℹ [2024-08-04 14:43:45.467275]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.468583]: Started.
#> ✔ [2024-08-04 14:43:45.469909]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.47157]: Done.
#> ℹ [2024-08-04 14:43:45.472896]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.474279]: Started.
#> ✔ [2024-08-04 14:43:45.475588]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.477351]: Done.
#> ℹ [2024-08-04 14:43:45.478764]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.480091]: Started.
#> ✔ [2024-08-04 14:43:45.481391]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.483066]: Done.
#> ℹ [2024-08-04 14:43:45.48439]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.485726]: Started.
#> ✔ [2024-08-04 14:43:45.486997]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.488648]: Done.
#> ℹ [2024-08-04 14:43:45.489991]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.491309]: Started.
#> ✔ [2024-08-04 14:43:45.492588]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.494275]: Done.
#> ℹ [2024-08-04 14:43:45.495591]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.4969]: Started.
#> ✔ [2024-08-04 14:43:45.498186]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.499831]: Done.
#> ℹ [2024-08-04 14:43:45.501151]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.502489]: Started.
#> ✔ [2024-08-04 14:43:45.50377]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.505447]: Done.
#> ℹ [2024-08-04 14:43:45.506762]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.508074]: Started.
#> ✔ [2024-08-04 14:43:45.509392]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.511062]: Done.
#> ℹ [2024-08-04 14:43:45.512389]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.513734]: Started.
#> ✔ [2024-08-04 14:43:45.515008]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.516662]: Done.
#> ℹ [2024-08-04 14:43:45.518005]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.519328]: Started.
#> ✔ [2024-08-04 14:43:45.520595]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.522288]: Done.
#> ℹ [2024-08-04 14:43:45.523604]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.524918]: Started.
#> ✔ [2024-08-04 14:43:45.526216]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.527871]: Done.
#> ℹ [2024-08-04 14:43:45.529196]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.530544]: Started.
#> ✔ [2024-08-04 14:43:45.531822]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.533508]: Done.
#> ℹ [2024-08-04 14:43:45.534899]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.53697]: Started.
#> ✔ [2024-08-04 14:43:45.539036]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.54162]: Done.
#> ℹ [2024-08-04 14:43:45.543637]: 0.007 secs elapsed.
#> ℹ [2024-08-04 14:43:45.545658]: Started.
#> ✔ [2024-08-04 14:43:45.54754]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.550031]: Done.
#> ℹ [2024-08-04 14:43:45.551645]: 0.006 secs elapsed.
#> ℹ [2024-08-04 14:43:45.552997]: Started.
#> ✔ [2024-08-04 14:43:45.554323]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.556015]: Done.
#> ℹ [2024-08-04 14:43:45.557384]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.558705]: Started.
#> ✔ [2024-08-04 14:43:45.559984]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.561693]: Done.
#> ℹ [2024-08-04 14:43:45.563038]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.56437]: Started.
#> ✔ [2024-08-04 14:43:45.565696]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.567377]: Done.
#> ℹ [2024-08-04 14:43:45.568715]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.570083]: Started.
#> ✔ [2024-08-04 14:43:45.571375]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.573057]: Done.
#> ℹ [2024-08-04 14:43:45.574432]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.575751]: Started.
#> ✔ [2024-08-04 14:43:45.577029]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.578738]: Done.
#> ℹ [2024-08-04 14:43:45.580073]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.58142]: Started.
#> ✔ [2024-08-04 14:43:45.582793]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.584493]: Done.
#> ℹ [2024-08-04 14:43:45.585868]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.587211]: Started.
#> ✔ [2024-08-04 14:43:45.588497]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.590195]: Done.
#> ℹ [2024-08-04 14:43:45.591526]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.592853]: Started.
#> ✔ [2024-08-04 14:43:45.594166]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.595851]: Done.
#> ℹ [2024-08-04 14:43:45.597184]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.598545]: Started.
#> ✔ [2024-08-04 14:43:45.599828]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.601526]: Done.
#> ℹ [2024-08-04 14:43:45.602881]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.60421]: Started.
#> ✔ [2024-08-04 14:43:45.605525]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.607209]: Done.
#> ℹ [2024-08-04 14:43:45.608536]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.609904]: Started.
#> ✔ [2024-08-04 14:43:45.611198]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.612882]: Done.
#> ℹ [2024-08-04 14:43:45.614251]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.615574]: Started.
#> ✔ [2024-08-04 14:43:45.616859]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.618562]: Done.
#> ℹ [2024-08-04 14:43:45.619891]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.621236]: Started.
#> ✔ [2024-08-04 14:43:45.62254]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.624241]: Done.
#> ℹ [2024-08-04 14:43:45.625607]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.626966]: Started.
#> ✔ [2024-08-04 14:43:45.628247]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.629965]: Done.
#> ℹ [2024-08-04 14:43:45.631307]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.632642]: Started.
#> ✔ [2024-08-04 14:43:45.633954]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.635637]: Done.
#> ℹ [2024-08-04 14:43:45.636997]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.638409]: Started.
#> ✔ [2024-08-04 14:43:45.639714]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.641437]: Done.
#> ℹ [2024-08-04 14:43:45.642796]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.644123]: Started.
#> ✔ [2024-08-04 14:43:45.645426]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.647132]: Done.
#> ℹ [2024-08-04 14:43:45.648463]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.649827]: Started.
#> ✔ [2024-08-04 14:43:45.651218]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.652932]: Done.
#> ℹ [2024-08-04 14:43:45.654304]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.655637]: Started.
#> ✔ [2024-08-04 14:43:45.656934]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.65866]: Done.
#> ℹ [2024-08-04 14:43:45.660005]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.661355]: Started.
#> ✔ [2024-08-04 14:43:45.662642]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.664362]: Done.
#> ℹ [2024-08-04 14:43:45.665746]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.667091]: Started.
#> ✔ [2024-08-04 14:43:45.668401]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.670128]: Done.
#> ℹ [2024-08-04 14:43:45.671493]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.67284]: Started.
#> ✔ [2024-08-04 14:43:45.674181]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.675897]: Done.
#> ℹ [2024-08-04 14:43:45.677297]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.678666]: Started.
#> ✔ [2024-08-04 14:43:45.679963]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.681702]: Done.
#> ℹ [2024-08-04 14:43:45.683065]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.684424]: Started.
#> ✔ [2024-08-04 14:43:45.685737]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.687428]: Done.
#> ℹ [2024-08-04 14:43:45.688786]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.690153]: Started.
#> ✔ [2024-08-04 14:43:45.691465]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.693155]: Done.
#> ℹ [2024-08-04 14:43:45.694536]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.695922]: Started.
#> ✔ [2024-08-04 14:43:45.697272]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.698989]: Done.
#> ℹ [2024-08-04 14:43:45.700346]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.701725]: Started.
#> ✔ [2024-08-04 14:43:45.703044]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.704787]: Done.
#> ℹ [2024-08-04 14:43:45.70618]: 0.004 secs elapsed.
#> ℹ [2024-08-04 14:43:45.707741]: Started.
#> ✔ [2024-08-04 14:43:45.709101]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.710989]: Done.
#> ℹ [2024-08-04 14:43:45.712427]: 0.005 secs elapsed.
#> ℹ [2024-08-04 14:43:45.713862]: Started.
#> ✔ [2024-08-04 14:43:45.715246]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.717021]: Done.
#> ℹ [2024-08-04 14:43:45.718471]: 0.005 secs elapsed.
#> ℹ [2024-08-04 14:43:45.719871]: Started.
#> ✔ [2024-08-04 14:43:45.721245]: Batch mode enabled.
#> ✔ [2024-08-04 14:43:45.723008]: Done.
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#> ✔ [2024-08-04 14:43:46.311955]: Done.
#> ℹ [2024-08-04 14:43:46.313308]: Cleaning results...
#> ✔ [2024-08-04 14:43:47.585721]: Outputing.
#> ℹ [2024-08-04 14:43:47.5881]: Total 3.027 mins elapsed.
#> ℹ [2024-08-04 14:43:47.58985]: Started.
#> ✔ [2024-08-04 14:43:47.592404]: NULL sample detected, aggregate mode enabled.
#> ℹ [2024-08-04 14:43:47.593808]: The summarized values will be stored in 'summary' element of result ggplot2 object.
#> ℹ [2024-08-04 14:43:47.619965]: Plotting.
#> ℹ [2024-08-04 14:43:47.65863]: 0.069 secs elapsed.
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#> ℹ [2024-08-04 14:43:47.663997]: Plotting.
#> ℹ [2024-08-04 14:43:47.696696]: 0.036 secs elapsed.
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#> ℹ [2024-08-04 14:43:47.702675]: Plotting.
#> ℹ [2024-08-04 14:43:47.735451]: 0.037 secs elapsed.
#> ℹ [2024-08-04 14:43:47.737528]: Started.
#> ✔ [2024-08-04 14:43:47.740271]: NULL sample detected, aggregate mode enabled.
#> ℹ [2024-08-04 14:43:47.741827]: The summarized values will be stored in 'summary' element of result ggplot2 object.
#> ℹ [2024-08-04 14:43:47.755065]: Plotting.
#> ℹ [2024-08-04 14:43:47.787239]: 0.05 secs elapsed.
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#> ℹ [2024-08-04 14:43:47.792217]: Plotting.
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#> ℹ [2024-08-04 14:43:47.857329]: Plotting.
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#> ℹ [2024-08-04 14:43:47.972116]: Plotting.
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#> ℹ [2024-08-04 14:43:48.004396]: Started.
#> ℹ [2024-08-04 14:43:48.022289]: Plotting.
#> ℹ [2024-08-04 14:43:48.052488]: 0.048 secs elapsed.
#> Warning: Removed 21 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).
#> Warning: Removed 21 rows containing missing values or values outside the scale range
#> (`geom_point()`).
# }