seg2bins: convert .seg files to match a chromInfo matrix

In SingerLab/gac: Genetic Analysis of Cells

convert .seg files to match a chromInfo matrix

Description

convert .seg files to match a chromInfo matrix

Usage

seg2bins(
  cnr,
  seg,
  sample.id = "ID",
  bin.id = NULL,
  coordinates.a = c("bin.chrom", "bin.start", "bin.end"),
  coordinates.b = c("chrom", "loc.start", "loc.end"),
  seg.mean.b = "seg.mean",
  multipcf = TRUE
)

Arguments

cnr	a cnr bundle
seg	a table in .seg format
sample.id	column name of sample ID in the .seg dat, default is "ID"
bin.id	column name containing a bin.id, defalt NULL, bin.id will be taken as the rownames of the data
coordinates.a	names of the columns containing chromosome, start, and end coordinates in the cnr
coordinates.b	names of the columns containing chromosome, start, and end coordinates in the seg data
seg.mean.b	name of column containg segment means default "seg.mean"
multipcf	weather to create a multi sample matrix of the .seg data or keep as run length encoding, akin to copynumber::multipcf, and copynumber::pcf, respectively. This function requires tidyr::pivot_wider

Examples

## Not run: 
data(cnr)
seg.data <- read.delim("path/to/data.seg")

binned.seg <- seg2bins(cnr, seg.data,
                       sample.id = "sampleID",
                       bin.id = "bin.id")

## End(Not run)

SingerLab/gac documentation built on March 29, 2025, 4:38 p.m.