get_absCopyNumber: Convert copy ratios into abosolute copy numbers when given...

In ShixiangWang/absCopyNumber: Tumor Purity, Ploidy and Absolute Copy Number Estimation

Description

This function converts copy ratios into abosolute copy numbers when the tumor purity and ploidy are provided by the user. The tumor purity and ploidy parameter should be taken from the result after running the "run_fromLocal" or "run_fromDF" etc. functions.

Usage

get_absCopyNumber(seg.data, alpha, tau, qmax = 7)

Arguments

seg.data	a data frame with five columns: "chrom", "loc.start", "loc.end", "eff.seg.len", "normalized.ratio".
alpha	tumor purity estimate
tau	tumor ploidy estimate
qmax	maximum allowed absolute copy number for any segments

Value

a data.frame columns:

rhat	expected copy ratio
CN	absolute copy number

Author(s)

Lei Bao

ShixiangWang/absCopyNumber documentation built on May 28, 2019, 5:42 p.m.