readSegmentationFile {PureCN} | R Documentation |
Read segmentation files produced by DNAcopy, CNVkit or GATK4.
readSegmentationFile( seg.file, sampleid, model.homozygous = FALSE, format, zero = FALSE, verbose = TRUE )
seg.file |
File with segmentation |
sampleid |
Sampleid, for segmentation files containing multiple samples |
model.homozygous |
Unless |
format |
File format. If missing, derived from the file extension. Currently DNAcopy, and GATK4 (ModelSegments) format supported. CNVkit uses DNAcopy format. |
zero |
Start position is 0-based. Default is |
verbose |
Verbose output. |
A data.frame
.
Markus Riester
seg.file <- system.file("extdata", "example_seg.txt", package = "PureCN") seg <- readSegmentationFile(seg.file, "Sample1")