R/get_sig_similarity.R
get_sig_similarity.RdThe reference signatures can be either a Signature object specified by Ref argument
or known COSMIC signatures specified by sig_db argument.
Two COSMIC databases are used for comparisons - "legacy" which includes 30 signaures,
and "SBS" - which includes updated/refined 65 signatures. This function is modified
from compareSignatures() in maftools package.
NOTE: all reference signatures are generated from gold standard tool:
SigProfiler.
get_sig_similarity(
Signature,
Ref = NULL,
sig_db = c("SBS", "legacy", "DBS", "ID", "TSB", "SBS_Nik_lab", "RS_Nik_lab",
"RS_BRCA560", "RS_USARC", "CNS_USARC", "CNS_TCGA", "CNS_TCGA176", "CNS_PCAWG176",
"SBS_hg19", "SBS_hg38", "SBS_mm9", "SBS_mm10", "DBS_hg19", "DBS_hg38", "DBS_mm9",
"DBS_mm10", "SBS_Nik_lab_Organ", "RS_Nik_lab_Organ", "latest_SBS_GRCh37",
"latest_DBS_GRCh37", "latest_ID_GRCh37", "latest_SBS_GRCh38", "latest_DBS_GRCh38",
"latest_SBS_mm9", "latest_DBS_mm9", "latest_SBS_mm10", "latest_DBS_mm10",
"latest_SBS_rn6", "latest_DBS_rn6", "latest_CN_GRCh37",
"latest_RNA-SBS_GRCh37", "latest_SV_GRCh38"),
db_type = c("", "human-exome", "human-genome"),
method = "cosine",
normalize = c("row", "feature"),
feature_setting = sigminer::CN.features,
set_order = TRUE,
pattern_to_rm = NULL,
verbose = TRUE
)a Signature object or a component-by-signature matrix/data.frame
(sum of each column is 1) or a normalized component-by-sample matrix/data.frame
(sum of each column is 1).
More please see examples.
default is NULL, can be a same object as Signature.
default 'legacy', it can be 'legacy' (for COSMIC v2 'SBS'),
'SBS', 'DBS', 'ID' and 'TSB' (for COSMIV v3.1 signatures)
for small scale mutations.
For more specific details, it can also be 'SBS_hg19', 'SBS_hg38',
'SBS_mm9', 'SBS_mm10', 'DBS_hg19', 'DBS_hg38', 'DBS_mm9', 'DBS_mm10' to use
COSMIC v3 reference signatures from Alexandrov, Ludmil B., et al. (2020) (reference #1).
In addition, it can be one of "SBS_Nik_lab_Organ", "RS_Nik_lab_Organ",
"SBS_Nik_lab", "RS_Nik_lab" to refer reference signatures from
Degasperi, Andrea, et al. (2020) (reference #2);
"RS_BRCA560", "RS_USARC" to reference signatures from BRCA560 and USARC cohorts;
"CNS_USARC" (40 categories), "CNS_TCGA" (48 categories) to reference copy number signatures from USARC cohort and TCGA;
"CNS_TCGA176" (176 categories) and "CNS_PCAWG176" (176 categories) to reference copy number signatures from PCAWG and TCGA separately.
UPDATE, the latest version of reference version can be automatically
downloaded and loaded from https://cancer.sanger.ac.uk/signatures/downloads/
when a option with latest_ prefix is specified (e.g. "latest_SBS_GRCh37").
Note: the signature profile for different genome builds are basically same.
And specific database (e.g. 'SBS_mm10') contains less signatures than all COSMIC
signatures (because some signatures are not detected from Alexandrov, Ludmil B., et al. (2020)).
For all available options, check the parameter setting.
only used when sig_db is enabled.
"" for keeping default, "human-exome" for transforming to exome frequency of component,
and "human-genome" for transforming to whole genome frequency of component.
Currently only works for 'SBS'.
default is 'cosine' for cosine similarity.
one of "row" and "feature". "row" is typically used for common mutational signatures. "feature" is designed by me to use when input are copy number signatures.
a data.frame used for classification.
Only used when method is "Wang" ("W").
Default is CN.features. Users can also set custom input with "feature",
"min" and "max" columns available. Valid features can be printed by
unique(CN.features$feature).
if TRUE, order the return similarity matrix.
patterns for removing some features/components in similarity
calculation. A vector of component name is also accepted.
The remove operation will be done after normalization. Default is NULL.
if TRUE, print extra info.
a list containing smilarities, aetiologies if available, best match and RSS.
Alexandrov, Ludmil B., et al. "The repertoire of mutational signatures in human cancer." Nature 578.7793 (2020): 94-101.
Degasperi, Andrea, et al. "A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies." Nature cancer 1.2 (2020): 249-263.
Steele, Christopher D., et al. "Undifferentiated sarcomas develop through distinct evolutionary pathways." Cancer Cell 35.3 (2019): 441-456.
Nik-Zainal, Serena, et al. "Landscape of somatic mutations in 560 breast cancer whole-genome sequences." Nature 534.7605 (2016): 47-54.
Steele, Christopher D., et al. "Signatures of copy number alterations in human cancer." Nature 606.7916 (2022): 984-991.
# Load mutational signature
load(system.file("extdata", "toy_mutational_signature.RData",
package = "sigminer", mustWork = TRUE
))
s1 <- get_sig_similarity(sig2, Ref = sig2)
#> -Comparing against Custom signatures/profiles
#> ---------------------------------------------
#> --Found Sig1 most similar to Sig1 [similarity: 1]
#> --Found Sig2 most similar to Sig2 [similarity: 1]
#> --Found Sig3 most similar to Sig3 [similarity: 1]
#> ------------------------------------
#> Return result invisiblely.
s1
#> $similarity
#> Sig1 Sig2 Sig3
#> Sig1 1 0 0
#> Sig2 0 1 0
#> Sig3 0 0 1
#>
#> $aetiology_db
#> [1] NA
#>
#> $best_match
#> $best_match$Sig1
#> $best_match$Sig1$aetiology
#> [1] NA
#>
#> $best_match$Sig1$best_match
#> [1] "Best match: Sig1 [similarity: 1]"
#>
#>
#> $best_match$Sig2
#> $best_match$Sig2$aetiology
#> [1] NA
#>
#> $best_match$Sig2$best_match
#> [1] "Best match: Sig2 [similarity: 1]"
#>
#>
#> $best_match$Sig3
#> $best_match$Sig3$aetiology
#> [1] NA
#>
#> $best_match$Sig3$best_match
#> [1] "Best match: Sig3 [similarity: 1]"
#>
#>
#>
#> $rss
#> Sig1 Sig2 Sig3
#> Sig1 0.000000 0.190663 0.430982
#> Sig2 0.190663 0.000000 0.347182
#> Sig3 0.430982 0.347182 0.000000
#>
#> attr(,"class")
#> [1] "similarity" "list"
s2 <- get_sig_similarity(sig2)
#> -Comparing against COSMIC signatures
#> ------------------------------------
#> --Found Sig1 most similar to SBS28
#> Aetiology: Unknown [similarity: 0.383]
#> --Found Sig2 most similar to SBS1
#> Aetiology: Spontaneous deamination of 5-methylcytosine (clock-like signature) [similarity: 0.868]
#> --Found Sig3 most similar to SBS10b
#> Aetiology: Polymerase epsilon exonuclease domain mutations [similarity: 0.865]
#> ------------------------------------
#> Return result invisiblely.
s2
#> $similarity
#> SBS28 SBS1 SBS10b SBS2 SBS3 SBS4 SBS5 SBS6 SBS7a SBS7b SBS7c SBS7d
#> Sig1 0.383 0.001 0.070 0.000 0.198 0.062 0.117 0.003 0.001 0.004 0.070 0.011
#> Sig2 0.023 0.868 0.080 0.141 0.340 0.219 0.492 0.836 0.220 0.281 0.095 0.111
#> Sig3 0.011 0.218 0.865 0.067 0.090 0.042 0.208 0.232 0.159 0.158 0.011 0.016
#> SBS8 SBS9 SBS10a SBS11 SBS12 SBS13 SBS14 SBS15 SBS16 SBS17a SBS17b SBS18
#> Sig1 0.094 0.350 0.011 0.001 0.011 0.007 0.004 0.010 0.046 0.011 0.373 0.043
#> Sig2 0.219 0.209 0.096 0.316 0.154 0.048 0.187 0.674 0.176 0.061 0.008 0.273
#> Sig3 0.043 0.079 0.019 0.014 0.075 0.021 0.033 0.118 0.033 0.040 0.005 0.096
#> SBS19 SBS20 SBS21 SBS22 SBS23 SBS24 SBS25 SBS26 SBS27 SBS29 SBS30 SBS31
#> Sig1 0.013 0.015 0.004 0.021 0.001 0.133 0.107 0.030 0.004 0.054 0.013 0.028
#> Sig2 0.317 0.255 0.103 0.054 0.355 0.260 0.393 0.178 0.081 0.282 0.389 0.304
#> Sig3 0.055 0.061 0.043 0.034 0.046 0.069 0.159 0.099 0.031 0.100 0.090 0.053
#> SBS32 SBS33 SBS34 SBS35 SBS36 SBS37 SBS38 SBS39 SBS40 SBS41 SBS42 SBS43
#> Sig1 0.016 0.006 0.007 0.061 0.014 0.112 0.014 0.249 0.201 0.232 0.031 0.051
#> Sig2 0.429 0.108 0.049 0.228 0.171 0.199 0.115 0.260 0.347 0.192 0.338 0.059
#> Sig3 0.067 0.036 0.008 0.023 0.065 0.073 0.015 0.075 0.101 0.056 0.049 0.030
#> SBS44 SBS45 SBS46 SBS47 SBS48 SBS49 SBS50 SBS51 SBS52 SBS53 SBS54 SBS55
#> Sig1 0.020 0.007 0.012 0.024 0.001 0.005 0.014 0.027 0.008 0.065 0.014 0.054
#> Sig2 0.417 0.127 0.219 0.100 0.027 0.068 0.237 0.184 0.051 0.135 0.170 0.076
#> Sig3 0.132 0.024 0.128 0.027 0.017 0.007 0.035 0.068 0.099 0.042 0.106 0.026
#> SBS56 SBS57 SBS58 SBS59 SBS60 SBS84 SBS85 SBS86 SBS87 SBS88 SBS89 SBS90
#> Sig1 0.029 0.186 0.051 0.026 0.025 0.032 0.057 0.111 0.119 0.166 0.141 0.040
#> Sig2 0.098 0.237 0.265 0.056 0.031 0.297 0.114 0.194 0.735 0.158 0.325 0.016
#> Sig3 0.049 0.042 0.034 0.003 0.006 0.080 0.027 0.069 0.228 0.051 0.066 0.004
#>
#> $aetiology_db
#> $aetiology_db[[1]]
#> [1] "Spontaneous deamination of 5-methylcytosine (clock-like signature)"
#> [2] "Activity of APOBEC family of cytidine deaminases"
#> [3] "Defective homologous recombination DNA damage repair"
#> [4] "Tobacco smoking"
#> [5] "Unknown (clock-like signature)"
#> [6] "Defective DNA mismatch repair"
#> [7] "Ultraviolet light exposure"
#> [8] "Ultraviolet light exposure"
#> [9] "Ultraviolet light exposure"
#> [10] "Ultraviolet light exposure"
#> [11] "Unknown"
#> [12] "Polimerase eta somatic hypermutation activity"
#> [13] "Polymerase epsilon exonuclease domain mutations"
#> [14] "Polymerase epsilon exonuclease domain mutations"
#> [15] "Temozolomide treatment"
#> [16] "Unknown"
#> [17] "Activity of APOBEC family of cytidine deaminases"
#> [18] "Concurrent polymerase epsilon mutation and defective DNA mismatch repair"
#> [19] "Defective DNA mismatch repair"
#> [20] "Unknown"
#> [21] "Unknown"
#> [22] "Unknown"
#> [23] "Damage by reactive oxygen species"
#> [24] "Unknown"
#> [25] "Concurrent POLD1 mutations and defective DNA mismatch repair"
#> [26] "Defective DNA mismatch repair"
#> [27] "Aristolochic acid exposure"
#> [28] "Unknown"
#> [29] "Aflatoxin exposure"
#> [30] "Chemotherapy treatment"
#> [31] "Defective DNA mismatch repair"
#> [32] "Possible sequencing artefact"
#> [33] "Unknown"
#> [34] "Tobacco chewing"
#> [35] "Defective DNA base excision repair due to NTHL1 mutations"
#> [36] "Platinum chemotherapy treatment"
#> [37] "Azathioprine treatment"
#> [38] "Unknown"
#> [39] "Unknown"
#> [40] "Platinum chemotherapy treatment"
#> [41] "Defective DNA base excision repair due to MUTYH mutations"
#> [42] "Unknown"
#> [43] "Indirect effect of ultraviolet light"
#> [44] "Unknown"
#> [45] "Unknown"
#> [46] "Unknown"
#> [47] "Haloalkane exposure"
#> [48] "Possible sequencing artefact"
#> [49] "Defective DNA mismatch repair"
#> [50] "Possible sequencing artefact"
#> [51] "Possible sequencing artefact"
#> [52] "Possible sequencing artefact"
#> [53] "Possible sequencing artefact"
#> [54] "Possible sequencing artefact"
#> [55] "Possible sequencing artefact"
#> [56] "Possible sequencing artefact"
#> [57] "Possible sequencing artefact"
#> [58] "Possible sequencing artefact"
#> [59] "Possible sequencing artefact"
#> [60] "Possible sequencing artefact"
#> [61] "Possible sequencing artefact"
#> [62] "Possible sequencing artefact"
#> [63] "Possible sequencing artefact"
#> [64] "Possible sequencing artefact"
#> [65] "Possible sequencing artefact"
#> [66] "Activity of activation-induced cytidine deaminase (AID)"
#> [67] "Indirect effects of activation-induced cytidine deaminase (AID)"
#> [68] "Unknown chemotherapy treatment"
#> [69] "Thiopurine chemotherapy treatment"
#> [70] "Colibactin exposure (E.coli bacteria carrying pks pathogenicity island)"
#> [71] "Unknown"
#> [72] "Duocarmycin exposure"
#>
#>
#> $best_match
#> $best_match$Sig1
#> $best_match$Sig1$aetiology
#> [1] "Unknown"
#>
#> $best_match$Sig1$best_match
#> [1] "Best match: SBS28 [similarity: 0.383]"
#>
#>
#> $best_match$Sig2
#> $best_match$Sig2$aetiology
#> [1] "Spontaneous deamination of 5-methylcytosine (clock-like signature)"
#>
#> $best_match$Sig2$best_match
#> [1] "Best match: SBS1 [similarity: 0.868]"
#>
#>
#> $best_match$Sig3
#> $best_match$Sig3$aetiology
#> [1] "Polymerase epsilon exonuclease domain mutations"
#>
#> $best_match$Sig3$best_match
#> [1] "Best match: SBS10b [similarity: 0.865]"
#>
#>
#>
#> $rss
#> SBS1 SBS2 SBS3 SBS4 SBS5 SBS6 SBS7a SBS7b
#> Sig1 0.369193 0.525837 0.133773 0.163154 0.142928 0.233049 0.329982 0.257810
#> Sig2 0.092395 0.401493 0.048795 0.069176 0.040832 0.029963 0.201746 0.129839
#> Sig3 0.412095 0.637387 0.296138 0.319891 0.281398 0.312334 0.410916 0.355830
#> SBS7c SBS7d SBS8 SBS9 SBS10a SBS10b SBS11 SBS12
#> Sig1 0.220593 0.259290 0.151807 0.121283 0.592288 0.339654 0.249398 0.184606
#> Sig2 0.139360 0.160424 0.062998 0.063645 0.483733 0.262953 0.116867 0.086949
#> Sig3 0.389688 0.412737 0.312035 0.305754 0.740139 0.073998 0.400920 0.325061
#> SBS13 SBS14 SBS15 SBS16 SBS17a SBS17b SBS18 SBS19
#> Sig1 0.384435 0.254322 0.251461 0.214292 0.361085 0.313559 0.181550 0.249426
#> Sig2 0.291947 0.141861 0.063769 0.116602 0.267755 0.388287 0.076398 0.119212
#> Sig3 0.531917 0.399662 0.366821 0.370351 0.501123 0.627313 0.321777 0.388976
#> SBS20 SBS21 SBS22 SBS23 SBS24 SBS25 SBS26 SBS27
#> Sig1 0.222261 0.237466 0.209514 0.250671 0.159083 0.145363 0.183891 0.284051
#> Sig2 0.106840 0.139489 0.123211 0.111862 0.070913 0.047459 0.086505 0.186965
#> Sig3 0.362647 0.379998 0.360274 0.390581 0.320568 0.289040 0.321052 0.428821
#> SBS28 SBS29 SBS30 SBS31 SBS32 SBS33 SBS34 SBS35
#> Sig1 0.251169 0.176705 0.217281 0.190168 0.198065 0.291670 0.326219 0.167234
#> Sig2 0.306440 0.073145 0.084439 0.077665 0.067240 0.189799 0.234887 0.071536
#> Sig3 0.546324 0.318320 0.348499 0.337970 0.339405 0.434520 0.481561 0.327852
#> SBS36 SBS37 SBS38 SBS39 SBS40 SBS41 SBS42 SBS43
#> Sig1 0.222163 0.155024 0.321314 0.131135 0.133988 0.141395 0.180887 0.219344
#> Sig2 0.118089 0.069663 0.219050 0.056606 0.048896 0.073695 0.067748 0.138797
#> Sig3 0.360991 0.312379 0.475377 0.302408 0.295547 0.319400 0.330777 0.377444
#> SBS44 SBS45 SBS46 SBS47 SBS48 SBS49 SBS50 SBS51
#> Sig1 0.182577 0.269907 0.176080 0.205584 0.674224 0.460338 0.197968 0.187056
#> Sig2 0.059625 0.166457 0.073658 0.114100 0.581815 0.360637 0.089241 0.088074
#> Sig3 0.310896 0.418861 0.306514 0.359080 0.817393 0.614301 0.347555 0.331071
#> SBS52 SBS53 SBS54 SBS55 SBS56 SBS57 SBS58 SBS59
#> Sig1 0.378140 0.250307 0.239819 0.256845 0.345687 0.165649 0.185579 0.405001
#> Sig2 0.285849 0.161257 0.133842 0.174820 0.251045 0.089001 0.081505 0.317869
#> Sig3 0.484724 0.407754 0.362176 0.417739 0.487844 0.345214 0.342362 0.569894
#> SBS60 SBS84 SBS85 SBS86 SBS87 SBS88 SBS89 SBS90
#> Sig1 0.571066 0.204442 0.175558 0.171859 0.180572 0.179788 0.141616 0.305934
#> Sig2 0.490093 0.089916 0.089645 0.086394 0.032164 0.109855 0.051612 0.231820
#> Sig3 0.735723 0.343883 0.335085 0.330248 0.296362 0.355069 0.302726 0.473481
#>
#> attr(,"class")
#> [1] "similarity" "list"
s3 <- get_sig_similarity(sig2, sig_db = "SBS")
#> -Comparing against COSMIC signatures
#> ------------------------------------
#> --Found Sig1 most similar to SBS28
#> Aetiology: Unknown [similarity: 0.383]
#> --Found Sig2 most similar to SBS1
#> Aetiology: Spontaneous deamination of 5-methylcytosine (clock-like signature) [similarity: 0.868]
#> --Found Sig3 most similar to SBS10b
#> Aetiology: Polymerase epsilon exonuclease domain mutations [similarity: 0.865]
#> ------------------------------------
#> Return result invisiblely.
s3
#> $similarity
#> SBS28 SBS1 SBS10b SBS2 SBS3 SBS4 SBS5 SBS6 SBS7a SBS7b SBS7c SBS7d
#> Sig1 0.383 0.001 0.070 0.000 0.198 0.062 0.117 0.003 0.001 0.004 0.070 0.011
#> Sig2 0.023 0.868 0.080 0.141 0.340 0.219 0.492 0.836 0.220 0.281 0.095 0.111
#> Sig3 0.011 0.218 0.865 0.067 0.090 0.042 0.208 0.232 0.159 0.158 0.011 0.016
#> SBS8 SBS9 SBS10a SBS11 SBS12 SBS13 SBS14 SBS15 SBS16 SBS17a SBS17b SBS18
#> Sig1 0.094 0.350 0.011 0.001 0.011 0.007 0.004 0.010 0.046 0.011 0.373 0.043
#> Sig2 0.219 0.209 0.096 0.316 0.154 0.048 0.187 0.674 0.176 0.061 0.008 0.273
#> Sig3 0.043 0.079 0.019 0.014 0.075 0.021 0.033 0.118 0.033 0.040 0.005 0.096
#> SBS19 SBS20 SBS21 SBS22 SBS23 SBS24 SBS25 SBS26 SBS27 SBS29 SBS30 SBS31
#> Sig1 0.013 0.015 0.004 0.021 0.001 0.133 0.107 0.030 0.004 0.054 0.013 0.028
#> Sig2 0.317 0.255 0.103 0.054 0.355 0.260 0.393 0.178 0.081 0.282 0.389 0.304
#> Sig3 0.055 0.061 0.043 0.034 0.046 0.069 0.159 0.099 0.031 0.100 0.090 0.053
#> SBS32 SBS33 SBS34 SBS35 SBS36 SBS37 SBS38 SBS39 SBS40 SBS41 SBS42 SBS43
#> Sig1 0.016 0.006 0.007 0.061 0.014 0.112 0.014 0.249 0.201 0.232 0.031 0.051
#> Sig2 0.429 0.108 0.049 0.228 0.171 0.199 0.115 0.260 0.347 0.192 0.338 0.059
#> Sig3 0.067 0.036 0.008 0.023 0.065 0.073 0.015 0.075 0.101 0.056 0.049 0.030
#> SBS44 SBS45 SBS46 SBS47 SBS48 SBS49 SBS50 SBS51 SBS52 SBS53 SBS54 SBS55
#> Sig1 0.020 0.007 0.012 0.024 0.001 0.005 0.014 0.027 0.008 0.065 0.014 0.054
#> Sig2 0.417 0.127 0.219 0.100 0.027 0.068 0.237 0.184 0.051 0.135 0.170 0.076
#> Sig3 0.132 0.024 0.128 0.027 0.017 0.007 0.035 0.068 0.099 0.042 0.106 0.026
#> SBS56 SBS57 SBS58 SBS59 SBS60 SBS84 SBS85 SBS86 SBS87 SBS88 SBS89 SBS90
#> Sig1 0.029 0.186 0.051 0.026 0.025 0.032 0.057 0.111 0.119 0.166 0.141 0.040
#> Sig2 0.098 0.237 0.265 0.056 0.031 0.297 0.114 0.194 0.735 0.158 0.325 0.016
#> Sig3 0.049 0.042 0.034 0.003 0.006 0.080 0.027 0.069 0.228 0.051 0.066 0.004
#>
#> $aetiology_db
#> $aetiology_db[[1]]
#> [1] "Spontaneous deamination of 5-methylcytosine (clock-like signature)"
#> [2] "Activity of APOBEC family of cytidine deaminases"
#> [3] "Defective homologous recombination DNA damage repair"
#> [4] "Tobacco smoking"
#> [5] "Unknown (clock-like signature)"
#> [6] "Defective DNA mismatch repair"
#> [7] "Ultraviolet light exposure"
#> [8] "Ultraviolet light exposure"
#> [9] "Ultraviolet light exposure"
#> [10] "Ultraviolet light exposure"
#> [11] "Unknown"
#> [12] "Polimerase eta somatic hypermutation activity"
#> [13] "Polymerase epsilon exonuclease domain mutations"
#> [14] "Polymerase epsilon exonuclease domain mutations"
#> [15] "Temozolomide treatment"
#> [16] "Unknown"
#> [17] "Activity of APOBEC family of cytidine deaminases"
#> [18] "Concurrent polymerase epsilon mutation and defective DNA mismatch repair"
#> [19] "Defective DNA mismatch repair"
#> [20] "Unknown"
#> [21] "Unknown"
#> [22] "Unknown"
#> [23] "Damage by reactive oxygen species"
#> [24] "Unknown"
#> [25] "Concurrent POLD1 mutations and defective DNA mismatch repair"
#> [26] "Defective DNA mismatch repair"
#> [27] "Aristolochic acid exposure"
#> [28] "Unknown"
#> [29] "Aflatoxin exposure"
#> [30] "Chemotherapy treatment"
#> [31] "Defective DNA mismatch repair"
#> [32] "Possible sequencing artefact"
#> [33] "Unknown"
#> [34] "Tobacco chewing"
#> [35] "Defective DNA base excision repair due to NTHL1 mutations"
#> [36] "Platinum chemotherapy treatment"
#> [37] "Azathioprine treatment"
#> [38] "Unknown"
#> [39] "Unknown"
#> [40] "Platinum chemotherapy treatment"
#> [41] "Defective DNA base excision repair due to MUTYH mutations"
#> [42] "Unknown"
#> [43] "Indirect effect of ultraviolet light"
#> [44] "Unknown"
#> [45] "Unknown"
#> [46] "Unknown"
#> [47] "Haloalkane exposure"
#> [48] "Possible sequencing artefact"
#> [49] "Defective DNA mismatch repair"
#> [50] "Possible sequencing artefact"
#> [51] "Possible sequencing artefact"
#> [52] "Possible sequencing artefact"
#> [53] "Possible sequencing artefact"
#> [54] "Possible sequencing artefact"
#> [55] "Possible sequencing artefact"
#> [56] "Possible sequencing artefact"
#> [57] "Possible sequencing artefact"
#> [58] "Possible sequencing artefact"
#> [59] "Possible sequencing artefact"
#> [60] "Possible sequencing artefact"
#> [61] "Possible sequencing artefact"
#> [62] "Possible sequencing artefact"
#> [63] "Possible sequencing artefact"
#> [64] "Possible sequencing artefact"
#> [65] "Possible sequencing artefact"
#> [66] "Activity of activation-induced cytidine deaminase (AID)"
#> [67] "Indirect effects of activation-induced cytidine deaminase (AID)"
#> [68] "Unknown chemotherapy treatment"
#> [69] "Thiopurine chemotherapy treatment"
#> [70] "Colibactin exposure (E.coli bacteria carrying pks pathogenicity island)"
#> [71] "Unknown"
#> [72] "Duocarmycin exposure"
#>
#>
#> $best_match
#> $best_match$Sig1
#> $best_match$Sig1$aetiology
#> [1] "Unknown"
#>
#> $best_match$Sig1$best_match
#> [1] "Best match: SBS28 [similarity: 0.383]"
#>
#>
#> $best_match$Sig2
#> $best_match$Sig2$aetiology
#> [1] "Spontaneous deamination of 5-methylcytosine (clock-like signature)"
#>
#> $best_match$Sig2$best_match
#> [1] "Best match: SBS1 [similarity: 0.868]"
#>
#>
#> $best_match$Sig3
#> $best_match$Sig3$aetiology
#> [1] "Polymerase epsilon exonuclease domain mutations"
#>
#> $best_match$Sig3$best_match
#> [1] "Best match: SBS10b [similarity: 0.865]"
#>
#>
#>
#> $rss
#> SBS1 SBS2 SBS3 SBS4 SBS5 SBS6 SBS7a SBS7b
#> Sig1 0.369193 0.525837 0.133773 0.163154 0.142928 0.233049 0.329982 0.257810
#> Sig2 0.092395 0.401493 0.048795 0.069176 0.040832 0.029963 0.201746 0.129839
#> Sig3 0.412095 0.637387 0.296138 0.319891 0.281398 0.312334 0.410916 0.355830
#> SBS7c SBS7d SBS8 SBS9 SBS10a SBS10b SBS11 SBS12
#> Sig1 0.220593 0.259290 0.151807 0.121283 0.592288 0.339654 0.249398 0.184606
#> Sig2 0.139360 0.160424 0.062998 0.063645 0.483733 0.262953 0.116867 0.086949
#> Sig3 0.389688 0.412737 0.312035 0.305754 0.740139 0.073998 0.400920 0.325061
#> SBS13 SBS14 SBS15 SBS16 SBS17a SBS17b SBS18 SBS19
#> Sig1 0.384435 0.254322 0.251461 0.214292 0.361085 0.313559 0.181550 0.249426
#> Sig2 0.291947 0.141861 0.063769 0.116602 0.267755 0.388287 0.076398 0.119212
#> Sig3 0.531917 0.399662 0.366821 0.370351 0.501123 0.627313 0.321777 0.388976
#> SBS20 SBS21 SBS22 SBS23 SBS24 SBS25 SBS26 SBS27
#> Sig1 0.222261 0.237466 0.209514 0.250671 0.159083 0.145363 0.183891 0.284051
#> Sig2 0.106840 0.139489 0.123211 0.111862 0.070913 0.047459 0.086505 0.186965
#> Sig3 0.362647 0.379998 0.360274 0.390581 0.320568 0.289040 0.321052 0.428821
#> SBS28 SBS29 SBS30 SBS31 SBS32 SBS33 SBS34 SBS35
#> Sig1 0.251169 0.176705 0.217281 0.190168 0.198065 0.291670 0.326219 0.167234
#> Sig2 0.306440 0.073145 0.084439 0.077665 0.067240 0.189799 0.234887 0.071536
#> Sig3 0.546324 0.318320 0.348499 0.337970 0.339405 0.434520 0.481561 0.327852
#> SBS36 SBS37 SBS38 SBS39 SBS40 SBS41 SBS42 SBS43
#> Sig1 0.222163 0.155024 0.321314 0.131135 0.133988 0.141395 0.180887 0.219344
#> Sig2 0.118089 0.069663 0.219050 0.056606 0.048896 0.073695 0.067748 0.138797
#> Sig3 0.360991 0.312379 0.475377 0.302408 0.295547 0.319400 0.330777 0.377444
#> SBS44 SBS45 SBS46 SBS47 SBS48 SBS49 SBS50 SBS51
#> Sig1 0.182577 0.269907 0.176080 0.205584 0.674224 0.460338 0.197968 0.187056
#> Sig2 0.059625 0.166457 0.073658 0.114100 0.581815 0.360637 0.089241 0.088074
#> Sig3 0.310896 0.418861 0.306514 0.359080 0.817393 0.614301 0.347555 0.331071
#> SBS52 SBS53 SBS54 SBS55 SBS56 SBS57 SBS58 SBS59
#> Sig1 0.378140 0.250307 0.239819 0.256845 0.345687 0.165649 0.185579 0.405001
#> Sig2 0.285849 0.161257 0.133842 0.174820 0.251045 0.089001 0.081505 0.317869
#> Sig3 0.484724 0.407754 0.362176 0.417739 0.487844 0.345214 0.342362 0.569894
#> SBS60 SBS84 SBS85 SBS86 SBS87 SBS88 SBS89 SBS90
#> Sig1 0.571066 0.204442 0.175558 0.171859 0.180572 0.179788 0.141616 0.305934
#> Sig2 0.490093 0.089916 0.089645 0.086394 0.032164 0.109855 0.051612 0.231820
#> Sig3 0.735723 0.343883 0.335085 0.330248 0.296362 0.355069 0.302726 0.473481
#>
#> attr(,"class")
#> [1] "similarity" "list"
# Set order for result similarity matrix
s4 <- get_sig_similarity(sig2, sig_db = "SBS", set_order = TRUE)
#> -Comparing against COSMIC signatures
#> ------------------------------------
#> --Found Sig1 most similar to SBS28
#> Aetiology: Unknown [similarity: 0.383]
#> --Found Sig2 most similar to SBS1
#> Aetiology: Spontaneous deamination of 5-methylcytosine (clock-like signature) [similarity: 0.868]
#> --Found Sig3 most similar to SBS10b
#> Aetiology: Polymerase epsilon exonuclease domain mutations [similarity: 0.865]
#> ------------------------------------
#> Return result invisiblely.
s4
#> $similarity
#> SBS28 SBS1 SBS10b SBS2 SBS3 SBS4 SBS5 SBS6 SBS7a SBS7b SBS7c SBS7d
#> Sig1 0.383 0.001 0.070 0.000 0.198 0.062 0.117 0.003 0.001 0.004 0.070 0.011
#> Sig2 0.023 0.868 0.080 0.141 0.340 0.219 0.492 0.836 0.220 0.281 0.095 0.111
#> Sig3 0.011 0.218 0.865 0.067 0.090 0.042 0.208 0.232 0.159 0.158 0.011 0.016
#> SBS8 SBS9 SBS10a SBS11 SBS12 SBS13 SBS14 SBS15 SBS16 SBS17a SBS17b SBS18
#> Sig1 0.094 0.350 0.011 0.001 0.011 0.007 0.004 0.010 0.046 0.011 0.373 0.043
#> Sig2 0.219 0.209 0.096 0.316 0.154 0.048 0.187 0.674 0.176 0.061 0.008 0.273
#> Sig3 0.043 0.079 0.019 0.014 0.075 0.021 0.033 0.118 0.033 0.040 0.005 0.096
#> SBS19 SBS20 SBS21 SBS22 SBS23 SBS24 SBS25 SBS26 SBS27 SBS29 SBS30 SBS31
#> Sig1 0.013 0.015 0.004 0.021 0.001 0.133 0.107 0.030 0.004 0.054 0.013 0.028
#> Sig2 0.317 0.255 0.103 0.054 0.355 0.260 0.393 0.178 0.081 0.282 0.389 0.304
#> Sig3 0.055 0.061 0.043 0.034 0.046 0.069 0.159 0.099 0.031 0.100 0.090 0.053
#> SBS32 SBS33 SBS34 SBS35 SBS36 SBS37 SBS38 SBS39 SBS40 SBS41 SBS42 SBS43
#> Sig1 0.016 0.006 0.007 0.061 0.014 0.112 0.014 0.249 0.201 0.232 0.031 0.051
#> Sig2 0.429 0.108 0.049 0.228 0.171 0.199 0.115 0.260 0.347 0.192 0.338 0.059
#> Sig3 0.067 0.036 0.008 0.023 0.065 0.073 0.015 0.075 0.101 0.056 0.049 0.030
#> SBS44 SBS45 SBS46 SBS47 SBS48 SBS49 SBS50 SBS51 SBS52 SBS53 SBS54 SBS55
#> Sig1 0.020 0.007 0.012 0.024 0.001 0.005 0.014 0.027 0.008 0.065 0.014 0.054
#> Sig2 0.417 0.127 0.219 0.100 0.027 0.068 0.237 0.184 0.051 0.135 0.170 0.076
#> Sig3 0.132 0.024 0.128 0.027 0.017 0.007 0.035 0.068 0.099 0.042 0.106 0.026
#> SBS56 SBS57 SBS58 SBS59 SBS60 SBS84 SBS85 SBS86 SBS87 SBS88 SBS89 SBS90
#> Sig1 0.029 0.186 0.051 0.026 0.025 0.032 0.057 0.111 0.119 0.166 0.141 0.040
#> Sig2 0.098 0.237 0.265 0.056 0.031 0.297 0.114 0.194 0.735 0.158 0.325 0.016
#> Sig3 0.049 0.042 0.034 0.003 0.006 0.080 0.027 0.069 0.228 0.051 0.066 0.004
#>
#> $aetiology_db
#> $aetiology_db[[1]]
#> [1] "Spontaneous deamination of 5-methylcytosine (clock-like signature)"
#> [2] "Activity of APOBEC family of cytidine deaminases"
#> [3] "Defective homologous recombination DNA damage repair"
#> [4] "Tobacco smoking"
#> [5] "Unknown (clock-like signature)"
#> [6] "Defective DNA mismatch repair"
#> [7] "Ultraviolet light exposure"
#> [8] "Ultraviolet light exposure"
#> [9] "Ultraviolet light exposure"
#> [10] "Ultraviolet light exposure"
#> [11] "Unknown"
#> [12] "Polimerase eta somatic hypermutation activity"
#> [13] "Polymerase epsilon exonuclease domain mutations"
#> [14] "Polymerase epsilon exonuclease domain mutations"
#> [15] "Temozolomide treatment"
#> [16] "Unknown"
#> [17] "Activity of APOBEC family of cytidine deaminases"
#> [18] "Concurrent polymerase epsilon mutation and defective DNA mismatch repair"
#> [19] "Defective DNA mismatch repair"
#> [20] "Unknown"
#> [21] "Unknown"
#> [22] "Unknown"
#> [23] "Damage by reactive oxygen species"
#> [24] "Unknown"
#> [25] "Concurrent POLD1 mutations and defective DNA mismatch repair"
#> [26] "Defective DNA mismatch repair"
#> [27] "Aristolochic acid exposure"
#> [28] "Unknown"
#> [29] "Aflatoxin exposure"
#> [30] "Chemotherapy treatment"
#> [31] "Defective DNA mismatch repair"
#> [32] "Possible sequencing artefact"
#> [33] "Unknown"
#> [34] "Tobacco chewing"
#> [35] "Defective DNA base excision repair due to NTHL1 mutations"
#> [36] "Platinum chemotherapy treatment"
#> [37] "Azathioprine treatment"
#> [38] "Unknown"
#> [39] "Unknown"
#> [40] "Platinum chemotherapy treatment"
#> [41] "Defective DNA base excision repair due to MUTYH mutations"
#> [42] "Unknown"
#> [43] "Indirect effect of ultraviolet light"
#> [44] "Unknown"
#> [45] "Unknown"
#> [46] "Unknown"
#> [47] "Haloalkane exposure"
#> [48] "Possible sequencing artefact"
#> [49] "Defective DNA mismatch repair"
#> [50] "Possible sequencing artefact"
#> [51] "Possible sequencing artefact"
#> [52] "Possible sequencing artefact"
#> [53] "Possible sequencing artefact"
#> [54] "Possible sequencing artefact"
#> [55] "Possible sequencing artefact"
#> [56] "Possible sequencing artefact"
#> [57] "Possible sequencing artefact"
#> [58] "Possible sequencing artefact"
#> [59] "Possible sequencing artefact"
#> [60] "Possible sequencing artefact"
#> [61] "Possible sequencing artefact"
#> [62] "Possible sequencing artefact"
#> [63] "Possible sequencing artefact"
#> [64] "Possible sequencing artefact"
#> [65] "Possible sequencing artefact"
#> [66] "Activity of activation-induced cytidine deaminase (AID)"
#> [67] "Indirect effects of activation-induced cytidine deaminase (AID)"
#> [68] "Unknown chemotherapy treatment"
#> [69] "Thiopurine chemotherapy treatment"
#> [70] "Colibactin exposure (E.coli bacteria carrying pks pathogenicity island)"
#> [71] "Unknown"
#> [72] "Duocarmycin exposure"
#>
#>
#> $best_match
#> $best_match$Sig1
#> $best_match$Sig1$aetiology
#> [1] "Unknown"
#>
#> $best_match$Sig1$best_match
#> [1] "Best match: SBS28 [similarity: 0.383]"
#>
#>
#> $best_match$Sig2
#> $best_match$Sig2$aetiology
#> [1] "Spontaneous deamination of 5-methylcytosine (clock-like signature)"
#>
#> $best_match$Sig2$best_match
#> [1] "Best match: SBS1 [similarity: 0.868]"
#>
#>
#> $best_match$Sig3
#> $best_match$Sig3$aetiology
#> [1] "Polymerase epsilon exonuclease domain mutations"
#>
#> $best_match$Sig3$best_match
#> [1] "Best match: SBS10b [similarity: 0.865]"
#>
#>
#>
#> $rss
#> SBS1 SBS2 SBS3 SBS4 SBS5 SBS6 SBS7a SBS7b
#> Sig1 0.369193 0.525837 0.133773 0.163154 0.142928 0.233049 0.329982 0.257810
#> Sig2 0.092395 0.401493 0.048795 0.069176 0.040832 0.029963 0.201746 0.129839
#> Sig3 0.412095 0.637387 0.296138 0.319891 0.281398 0.312334 0.410916 0.355830
#> SBS7c SBS7d SBS8 SBS9 SBS10a SBS10b SBS11 SBS12
#> Sig1 0.220593 0.259290 0.151807 0.121283 0.592288 0.339654 0.249398 0.184606
#> Sig2 0.139360 0.160424 0.062998 0.063645 0.483733 0.262953 0.116867 0.086949
#> Sig3 0.389688 0.412737 0.312035 0.305754 0.740139 0.073998 0.400920 0.325061
#> SBS13 SBS14 SBS15 SBS16 SBS17a SBS17b SBS18 SBS19
#> Sig1 0.384435 0.254322 0.251461 0.214292 0.361085 0.313559 0.181550 0.249426
#> Sig2 0.291947 0.141861 0.063769 0.116602 0.267755 0.388287 0.076398 0.119212
#> Sig3 0.531917 0.399662 0.366821 0.370351 0.501123 0.627313 0.321777 0.388976
#> SBS20 SBS21 SBS22 SBS23 SBS24 SBS25 SBS26 SBS27
#> Sig1 0.222261 0.237466 0.209514 0.250671 0.159083 0.145363 0.183891 0.284051
#> Sig2 0.106840 0.139489 0.123211 0.111862 0.070913 0.047459 0.086505 0.186965
#> Sig3 0.362647 0.379998 0.360274 0.390581 0.320568 0.289040 0.321052 0.428821
#> SBS28 SBS29 SBS30 SBS31 SBS32 SBS33 SBS34 SBS35
#> Sig1 0.251169 0.176705 0.217281 0.190168 0.198065 0.291670 0.326219 0.167234
#> Sig2 0.306440 0.073145 0.084439 0.077665 0.067240 0.189799 0.234887 0.071536
#> Sig3 0.546324 0.318320 0.348499 0.337970 0.339405 0.434520 0.481561 0.327852
#> SBS36 SBS37 SBS38 SBS39 SBS40 SBS41 SBS42 SBS43
#> Sig1 0.222163 0.155024 0.321314 0.131135 0.133988 0.141395 0.180887 0.219344
#> Sig2 0.118089 0.069663 0.219050 0.056606 0.048896 0.073695 0.067748 0.138797
#> Sig3 0.360991 0.312379 0.475377 0.302408 0.295547 0.319400 0.330777 0.377444
#> SBS44 SBS45 SBS46 SBS47 SBS48 SBS49 SBS50 SBS51
#> Sig1 0.182577 0.269907 0.176080 0.205584 0.674224 0.460338 0.197968 0.187056
#> Sig2 0.059625 0.166457 0.073658 0.114100 0.581815 0.360637 0.089241 0.088074
#> Sig3 0.310896 0.418861 0.306514 0.359080 0.817393 0.614301 0.347555 0.331071
#> SBS52 SBS53 SBS54 SBS55 SBS56 SBS57 SBS58 SBS59
#> Sig1 0.378140 0.250307 0.239819 0.256845 0.345687 0.165649 0.185579 0.405001
#> Sig2 0.285849 0.161257 0.133842 0.174820 0.251045 0.089001 0.081505 0.317869
#> Sig3 0.484724 0.407754 0.362176 0.417739 0.487844 0.345214 0.342362 0.569894
#> SBS60 SBS84 SBS85 SBS86 SBS87 SBS88 SBS89 SBS90
#> Sig1 0.571066 0.204442 0.175558 0.171859 0.180572 0.179788 0.141616 0.305934
#> Sig2 0.490093 0.089916 0.089645 0.086394 0.032164 0.109855 0.051612 0.231820
#> Sig3 0.735723 0.343883 0.335085 0.330248 0.296362 0.355069 0.302726 0.473481
#>
#> attr(,"class")
#> [1] "similarity" "list"
## Remove some components
## in similarity calculation
s5 <- get_sig_similarity(sig2,
Ref = sig2,
pattern_to_rm = c("T[T>G]C", "T[T>G]G", "T[T>G]T")
)
#> -Comparing against Custom signatures/profiles
#> ---------------------------------------------
#> --Found Sig1 most similar to Sig1 [similarity: 1]
#> --Found Sig2 most similar to Sig2 [similarity: 1]
#> --Found Sig3 most similar to Sig3 [similarity: 1]
#> ------------------------------------
#> Return result invisiblely.
s5
#> $similarity
#> Sig1 Sig2 Sig3
#> Sig1 1 0 0
#> Sig2 0 1 0
#> Sig3 0 0 1
#>
#> $aetiology_db
#> [1] NA
#>
#> $best_match
#> $best_match$Sig1
#> $best_match$Sig1$aetiology
#> [1] NA
#>
#> $best_match$Sig1$best_match
#> [1] "Best match: Sig1 [similarity: 1]"
#>
#>
#> $best_match$Sig2
#> $best_match$Sig2$aetiology
#> [1] NA
#>
#> $best_match$Sig2$best_match
#> [1] "Best match: Sig2 [similarity: 1]"
#>
#>
#> $best_match$Sig3
#> $best_match$Sig3$aetiology
#> [1] NA
#>
#> $best_match$Sig3$best_match
#> [1] "Best match: Sig3 [similarity: 1]"
#>
#>
#>
#> $rss
#> Sig1 Sig2 Sig3
#> Sig1 0.000000 0.176481 0.416715
#> Sig2 0.176481 0.000000 0.347079
#> Sig3 0.416715 0.347079 0.000000
#>
#> attr(,"class")
#> [1] "similarity" "list"
## Same to DBS and ID signatures
x1 <- get_sig_db("DBS_hg19")
x2 <- get_sig_db("DBS_hg38")
s6 <- get_sig_similarity(x1$db, x2$db)
#> -Comparing against Custom signatures/profiles
#> ---------------------------------------------
#> --Found DBS1 most similar to DBS1 [similarity: 1]
#> --Found DBS2 most similar to DBS2 [similarity: 1]
#> --Found DBS3 most similar to DBS3 [similarity: 1]
#> --Found DBS4 most similar to DBS4 [similarity: 1]
#> --Found DBS5 most similar to DBS5 [similarity: 1]
#> --Found DBS6 most similar to DBS6 [similarity: 1]
#> --Found DBS7 most similar to DBS7 [similarity: 1]
#> --Found DBS8 most similar to DBS8 [similarity: 1]
#> --Found DBS9 most similar to DBS9 [similarity: 1]
#> --Found DBS10 most similar to DBS10 [similarity: 1]
#> --Found DBS11 most similar to DBS11 [similarity: 1]
#> ------------------------------------
#> Return result invisiblely.
s6
#> $similarity
#> DBS1 DBS2 DBS3 DBS4 DBS5 DBS6 DBS7 DBS8 DBS9 DBS10 DBS11
#> DBS1 1.000 0.004 0.006 0.002 0.002 0.004 0.011 0.018 0.012 0.059 0.905
#> DBS2 0.004 1.000 0.040 0.012 0.011 0.028 0.007 0.112 0.029 0.043 0.018
#> DBS3 0.006 0.039 1.000 0.077 0.074 0.095 0.070 0.083 0.121 0.635 0.042
#> DBS4 0.002 0.012 0.077 1.000 0.060 0.106 0.070 0.115 0.098 0.045 0.013
#> DBS5 0.002 0.011 0.074 0.060 1.000 0.077 0.025 0.086 0.032 0.031 0.026
#> DBS6 0.004 0.028 0.095 0.106 0.077 1.000 0.041 0.090 0.093 0.040 0.049
#> DBS7 0.011 0.007 0.070 0.070 0.025 0.041 1.000 0.171 0.101 0.069 0.045
#> DBS8 0.018 0.111 0.083 0.115 0.086 0.090 0.171 1.000 0.241 0.071 0.049
#> DBS9 0.012 0.029 0.122 0.098 0.032 0.093 0.101 0.242 1.000 0.081 0.192
#> DBS10 0.058 0.042 0.629 0.044 0.031 0.039 0.068 0.070 0.080 1.000 0.090
#> DBS11 0.903 0.018 0.042 0.013 0.026 0.050 0.045 0.049 0.193 0.092 1.000
#>
#> $aetiology_db
#> [1] NA
#>
#> $best_match
#> $best_match$DBS1
#> $best_match$DBS1$aetiology
#> [1] NA
#>
#> $best_match$DBS1$best_match
#> [1] "Best match: DBS1 [similarity: 1]"
#>
#>
#> $best_match$DBS2
#> $best_match$DBS2$aetiology
#> [1] NA
#>
#> $best_match$DBS2$best_match
#> [1] "Best match: DBS2 [similarity: 1]"
#>
#>
#> $best_match$DBS3
#> $best_match$DBS3$aetiology
#> [1] NA
#>
#> $best_match$DBS3$best_match
#> [1] "Best match: DBS3 [similarity: 1]"
#>
#>
#> $best_match$DBS4
#> $best_match$DBS4$aetiology
#> [1] NA
#>
#> $best_match$DBS4$best_match
#> [1] "Best match: DBS4 [similarity: 1]"
#>
#>
#> $best_match$DBS5
#> $best_match$DBS5$aetiology
#> [1] NA
#>
#> $best_match$DBS5$best_match
#> [1] "Best match: DBS5 [similarity: 1]"
#>
#>
#> $best_match$DBS6
#> $best_match$DBS6$aetiology
#> [1] NA
#>
#> $best_match$DBS6$best_match
#> [1] "Best match: DBS6 [similarity: 1]"
#>
#>
#> $best_match$DBS7
#> $best_match$DBS7$aetiology
#> [1] NA
#>
#> $best_match$DBS7$best_match
#> [1] "Best match: DBS7 [similarity: 1]"
#>
#>
#> $best_match$DBS8
#> $best_match$DBS8$aetiology
#> [1] NA
#>
#> $best_match$DBS8$best_match
#> [1] "Best match: DBS8 [similarity: 1]"
#>
#>
#> $best_match$DBS9
#> $best_match$DBS9$aetiology
#> [1] NA
#>
#> $best_match$DBS9$best_match
#> [1] "Best match: DBS9 [similarity: 1]"
#>
#>
#> $best_match$DBS10
#> $best_match$DBS10$aetiology
#> [1] NA
#>
#> $best_match$DBS10$best_match
#> [1] "Best match: DBS10 [similarity: 1]"
#>
#>
#> $best_match$DBS11
#> $best_match$DBS11$aetiology
#> [1] NA
#>
#> $best_match$DBS11$best_match
#> [1] "Best match: DBS11 [similarity: 1]"
#>
#>
#>
#> $rss
#> DBS1 DBS2 DBS3 DBS4 DBS5 DBS6 DBS7 DBS8
#> DBS1 0.000001 1.274845 0.811053 0.998088 1.008771 0.872793 0.819496 0.880769
#> DBS2 1.275535 0.000000 0.600070 0.793207 0.803739 0.662650 0.624209 0.630502
#> DBS3 0.812674 0.601145 0.000002 0.315999 0.326705 0.194041 0.151426 0.212984
#> DBS4 0.999962 0.794450 0.316209 0.000008 0.502262 0.359550 0.328095 0.371142
#> DBS5 1.010232 0.804571 0.326510 0.501858 0.000000 0.379854 0.351277 0.391872
#> DBS6 0.874332 0.663593 0.193905 0.359186 0.379901 0.000001 0.215563 0.266499
#> DBS7 0.821218 0.625222 0.151482 0.327914 0.351505 0.215728 0.000001 0.202510
#> DBS8 0.882588 0.632074 0.213066 0.371010 0.392142 0.266719 0.202557 0.000000
#> DBS9 0.787424 0.583931 0.112796 0.291311 0.316967 0.174142 0.125736 0.164031
#> DBS10 0.849672 0.666045 0.090767 0.392899 0.408140 0.274887 0.220104 0.282443
#> DBS11 0.301043 0.668610 0.204577 0.394314 0.399372 0.261241 0.214536 0.278222
#> DBS9 DBS10 DBS11
#> DBS1 0.786055 0.845623 0.298327
#> DBS2 0.583217 0.662877 0.668733
#> DBS3 0.113112 0.088468 0.205699
#> DBS4 0.291864 0.391130 0.395667
#> DBS5 0.317090 0.405990 0.400337
#> DBS6 0.174335 0.272804 0.262280
#> DBS7 0.126095 0.218165 0.215727
#> DBS8 0.164482 0.280516 0.279475
#> DBS9 0.000001 0.184824 0.158164
#> DBS10 0.187116 0.000010 0.261218
#> DBS11 0.157264 0.257965 0.000004
#>
#> attr(,"class")
#> [1] "similarity" "list"