continuousSegments: Make continuous segments and split segments spanning the...

In arnevpladsen/CARMA: Calculate CARMA scores

Description

This function will not be called directly by the user. The function is used by the CARMA function to reformat input copy number profiles by extending segments flanked by gaps and by splitting segments spanning the centromere. The function can also optionally exclude the X chromosome.

Usage

continuousSegments(seg, hg, exclude.x.chrom = F)

Arguments

seg	a data frame containing the copy number profile of a single sample.
hg	a data frame containing start and end positions of chromosome arms: hg19 or hg38.
exclude.x.chrom	if exclude.x.chrom=TRUE, the X chromosome is excluded in the output file.

Value

A data frame containing formatted segment start and end positions.

Examples

segment <- test.data[[1]]
continuousSegments(segment, hg19, exclude.x.chrom=F)

arnevpladsen/CARMA documentation built on Dec. 19, 2021, 4:39 a.m.