callWcna: Call Whole chromosome aneuploidies from segments based on a...

In sdangelis/sdamisc: A convenience package bringing together commonly used R functions

Call Whole chromosome aneuploidies from segments based on a threshold

Description

Call Whole chromosome aneuploidies from segments based on a threshold

Usage

callWcna(segs, chr, threshold = 0.95)

Arguments

segs	data frame with CNA length, chromosome and direction ("gain","loss","normal") columns
chr	the chromosome of interest. must match the format of the segment table
threshold	float, the fraction of the chromosome needed to be in a direction to call. Default = 0.95

Value

"gain", "loss", "normal" or NA, a string with the status of the chromosome

Note

This function estimates the length of the genome from the length of all segments in the table

if the given chromosome is not found returns NA.

thresholds below < 0.5 always return gains as long as it passes it, regardless of whether there are more losses.

See Also

callArmCna fractionAltered

sdangelis/sdamisc documentation built on Sept. 21, 2022, 11:45 a.m.