callAlterationsFromSegmentation: Calling of amplifications and deletions from segmentations

View source: R/callAlterations.R

callAlterationsFromSegmentationR Documentation

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 Jan. 16, 2024, 1:49 a.m.