compare_purple_gene_files: Compare two PURPLE gene CNV files

In pdiakumis/woofr: Helper R Functions for woof

Compare two PURPLE gene CNV files

Description

Compares two PURPLE gene.cnv (or cnv.gene.tsv) files.

Usage

compare_purple_gene_files(
  cnv1,
  cnv2,
  out_cn_diff,
  out_coord_diff,
  threshold = 0.1
)

Arguments

cnv1	Path to first PURPLE gene.cnv (or cnv.gene.tsv) file.
cnv2	Path to second PURPLE gene.cnv (or cnv.gene.tsv) file ('TRUTHSET').
out_cn_diff	Path to write genes with copy number differences between the two runs - needs to be a writable directory.
out_coord_diff	Path to write genes with different coordinates between the two runs - needs to be a writable directory.
threshold	Numeric. Copy number differences smaller than this value are not reported.

Value

Writes results from the comparison to out_cn_diff and out_coord_diff.

Examples

cnv1 <- system.file("extdata", "cnv/sample_A.purple.gene.cnv", package = "woofr")
cnv2 <- system.file("extdata", "cnv/sample_B.purple.cnv.gene.tsv", package = "woofr")
out1 <- tempfile()
out2 <- tempfile()
compare_purple_gene_files(cnv1, cnv2, out1, out2, threshold = 0.1)

pdiakumis/woofr documentation built on Jan. 4, 2024, 11:22 a.m.