Transform Copy Number Table
a CopyNumber object or a data.frame containing
at least 'chromosome', 'start', 'end', 'segVal', 'sample' these columns.
genome build version, used when data is a data.frame, should be 'hg19' or 'hg38'.
annotation data type used for constructing matrix.
Optionally, a (scalar) value that specifies what each
value should be filled in with when missing.
This can be a named list if you want to apply different fill values to different value columns.
Optionally, a function applied to the value in each cell
in the output. You will typically use this when the combination of
id_cols and names_from columns does not uniquely identify an
observation.
This can be a named list if you want to apply different aggregations
to different values_from columns.
an integer to control the resolution.
When it is 1 (default), compute frequency in each cytoband.
When it is 2, use compute frequency in each half cytoband.
a data.table.
# \donttest{
load(system.file("extdata", "toy_copynumber.RData",
package = "sigminer", mustWork = TRUE
))
# Compute the mean segVal in each cytoband
x <- transform_seg_table(cn, resolution_factor = 1)
x
#> chromosome start end label stain TCGA-05-4417-01A-22D-1854-01
#> <char> <int> <int> <char> <char> <num>
#> 1: chr1 2300001 5400000 p36.32 gpos25 2
#> 2: chr1 5400001 7200000 p36.31 gneg 2
#> 3: chr1 7200001 9200000 p36.23 gpos25 2
#> 4: chr1 9200001 12700000 p36.22 gneg 2
#> 5: chr1 12700001 16200000 p36.21 gpos50 2
#> ---
#> 782: chr9 130300001 133500000 q34.11 gneg 3
#> 783: chr9 133500001 134000000 q34.12 gpos25 3
#> 784: chr9 134000001 135900000 q34.13 gneg 3
#> 785: chr9 135900001 137400000 q34.2 gpos25 3
#> 786: chr9 137400001 141213431 q34.3 gneg 3
#> TCGA-06-0644-01A-02D-0310-01 TCGA-19-2621-01B-01D-0911-01
#> <num> <num>
#> 1: 2 2
#> 2: 2 2
#> 3: 2 2
#> 4: 2 2
#> 5: 2 2
#> ---
#> 782: 2 2
#> 783: 2 2
#> 784: 2 2
#> 785: 2 2
#> 786: 2 2
#> TCGA-26-6174-01A-21D-1842-01 TCGA-99-7458-01A-11D-2035-01
#> <num> <num>
#> 1: 2 3
#> 2: 2 3
#> 3: 2 3
#> 4: 2 3
#> 5: 2 3
#> ---
#> 782: 3 2
#> 783: 3 2
#> 784: 3 2
#> 785: 3 2
#> 786: 3 2
#> TCGA-A5-A0G2-01A-11D-A042-01 TCGA-A8-A07S-01A-11D-A036-01
#> <num> <num>
#> 1: 1 2
#> 2: 1 2
#> 3: 1 2
#> 4: 1 2
#> 5: 1 2
#> ---
#> 782: 2 2
#> 783: 2 2
#> 784: 2 2
#> 785: 2 2
#> 786: 2 2
#> TCGA-B6-A0X5-01A-21D-A107-01 TCGA-CV-7432-01A-11D-2128-01
#> <num> <num>
#> 1: 2 2
#> 2: 2 2
#> 3: 2 2
#> 4: 2 2
#> 5: 2 2
#> ---
#> 782: 2 3
#> 783: 2 3
#> 784: 2 3
#> 785: 2 3
#> 786: 2 3
#> TCGA-DF-A2KN-01A-11D-A17U-01
#> <num>
#> 1: 2
#> 2: 2
#> 3: 2
#> 4: 2
#> 5: 2
#> ---
#> 782: 2
#> 783: 2
#> 784: 2
#> 785: 2
#> 786: 2
# Compute the mean segVal in each half-cytoband
x2 <- transform_seg_table(cn, resolution_factor = 2)
x2
#> chromosome start end label
#> <char> <num> <num> <char>
#> 1: chr1 2300001 3849999 p36.32-chunk-1
#> 2: chr1 3850000 5400000 p36.32-chunk-2
#> 3: chr1 5400001 6299999 p36.31-chunk-1
#> 4: chr1 6300000 7200000 p36.31-chunk-2
#> 5: chr1 7200001 8199999 p36.23-chunk-1
#> ---
#> 1561: chr9 134950000 135900000 q34.13-chunk-2
#> 1562: chr9 135900001 136649999 q34.2-chunk-1
#> 1563: chr9 136650000 137400000 q34.2-chunk-2
#> 1564: chr9 137400001 139306715 q34.3-chunk-1
#> 1565: chr9 139306716 141213431 q34.3-chunk-2
#> TCGA-05-4417-01A-22D-1854-01 TCGA-06-0644-01A-02D-0310-01
#> <num> <num>
#> 1: 2 2
#> 2: 2 2
#> 3: 2 2
#> 4: 2 2
#> 5: 2 2
#> ---
#> 1561: 3 2
#> 1562: 3 2
#> 1563: 3 2
#> 1564: 3 2
#> 1565: 3 2
#> TCGA-19-2621-01B-01D-0911-01 TCGA-26-6174-01A-21D-1842-01
#> <num> <num>
#> 1: 2 2
#> 2: 2 2
#> 3: 2 2
#> 4: 2 2
#> 5: 2 2
#> ---
#> 1561: 2 3
#> 1562: 2 3
#> 1563: 2 3
#> 1564: 2 3
#> 1565: 2 3
#> TCGA-99-7458-01A-11D-2035-01 TCGA-A5-A0G2-01A-11D-A042-01
#> <num> <num>
#> 1: 3 1
#> 2: 3 1
#> 3: 3 1
#> 4: 3 1
#> 5: 3 1
#> ---
#> 1561: 2 2
#> 1562: 2 2
#> 1563: 2 2
#> 1564: 2 2
#> 1565: 2 2
#> TCGA-A8-A07S-01A-11D-A036-01 TCGA-B6-A0X5-01A-21D-A107-01
#> <num> <num>
#> 1: 2 2
#> 2: 2 2
#> 3: 2 2
#> 4: 2 2
#> 5: 2 2
#> ---
#> 1561: 2 2
#> 1562: 2 2
#> 1563: 2 2
#> 1564: 2 2
#> 1565: 2 2
#> TCGA-CV-7432-01A-11D-2128-01 TCGA-DF-A2KN-01A-11D-A17U-01
#> <num> <num>
#> 1: 2 2
#> 2: 2 2
#> 3: 2 2
#> 4: 2 2
#> 5: 2 2
#> ---
#> 1561: 3 2
#> 1562: 3 2
#> 1563: 3 2
#> 1564: 3 2
#> 1565: 3 2
# }