callAlterationsFromSegmentation: Calling of amplifications and deletions from segmentations

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

Calling of amplifications and deletions from segmentations

Description

This function can be used to obtain gene-level copy number calls from segmentations. This is useful for comparing PureCN's segmentations with segmentations obtained by different tools on the gene-level. Segmentation file can contain multiple samples.

Usage

callAlterationsFromSegmentation(
  sampleid,
  chr,
  start,
  end,
  num.mark = NA,
  seg.mean,
  C,
  interval.file,
  fun.focal = findFocal,
  args.focal = list(),
  ...
)

Arguments

sampleid	The sampleid column in the segmentation file.
chr	The chromosome column.
start	The start positions of the segments.
end	The end positions of the segments.
num.mark	Optionally, the number of probes or markers in each segment.
seg.mean	The segment mean.
C	The segment integer copy number.
interval.file	A mapping file that assigns GC content and gene symbols to each exon in the coverage files. Used for generating gene-level calls. First column in format CHR:START-END. Second column GC content (0 to 1). Third column gene symbol. This file is generated with the preprocessIntervals function.
fun.focal	Function for identifying focal amplifications. Defaults to findFocal.
args.focal	Arguments for focal amplification function.
...	Arguments passed to callAlterations.

Value

A list of callAlterations data.frame objects, one for each sample.

Author(s)

Markus Riester

Examples

data(purecn.example.output)
seg <- purecn.example.output$results[[1]]$seg
interval.file <- system.file("extdata", "example_intervals.txt",
        package = "PureCN")

calls <- callAlterationsFromSegmentation(sampleid = seg$ID, chr = seg$chrom,
    start = seg$loc.start, end = seg$loc.end, num.mark = seg$num.mark,
    seg.mean = seg$seg.mean, C = seg$C, interval.file = interval.file)

lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.