callArmCna: Wrapper around CallWcna() that calls chromosome arm...

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

Wrapper around CallWcna() that calls chromosome arm aneuploidies

Description

Wrapper around CallWcna() that calls chromosome arm aneuploidies

Usage

callArmCna(segs, chr, threshold = 0.95, arms)

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 = 0.9
arms	a table with the list of p and q arm location

Value

a named vector with the arm and "gain", "loss", "normal" or NA.

Note

This assumes that there is a gap around the centromere and that no segment can ever overlaps it.

for full documentation see callWcna.

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

See Also

callWcna

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