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Read PURPLE Somatic CNVs for HRDetect

Source: R/hrdetect.R
hrdetect_read_purple_cnv.Rd

Reads PURPLE somatic CNVs for use with HRDetect.

Usage

hrdetect_read_purple_cnv(x)

Arguments

x

Path to purple.cnv.somatic.tsv file.

Value

Tibble containing following columns:

  • chromosome, start, end

  • copyNumber (total)

  • minorAllelePloidy

Examples

x <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
(cnv <- hrdetect_read_purple_cnv(x))
#> # A tibble: 59 × 5
#>    Chromosome chromStart  chromEnd total.copy.number.in…¹ minor.copy.number.in…²
#>    <chr>           <int>     <int>                  <dbl>                  <dbl>
#>  1 1                   1 123605522                   1.02                 0.0184
#>  2 1           123605523 200044314                   1.99                 0.989 
#>  3 1           200044315 200044570                   2.83                 0.993 
#>  4 1           200044571 248956422                   2.01                 0.993 
#>  5 2                   1  93139350                   2.01                 0.994 
#>  6 2            93139351 219955359                   2.00                 0.996 
#>  7 2           219955360 225225069                   1.02                 0.0196
#>  8 2           225225070 242193529                   2.03                 0.990 
#>  9 3                   1  92214015                   1.03                 0.0176
#> 10 3            92214016 198295559                   2.00                 0.992 
#> # ℹ 49 more rows
#> # ℹ abbreviated names: ¹​total.copy.number.inTumour, ²​minor.copy.number.inTumour