logRlogORspider: Plot segment logR-logOR summary statistics

In mskcc/facets: Cellular Fraction and Copy Numbers from Tumor Sequencing

Description

Plots copy number log-ratio, variant allele log-odds ratio as well as the copy number and cellular fraction fits.

Usage

  logRlogORspider(cncf, dipLogR=0, nfrac=0.005)

Arguments

cncf	Copy number and cellular fraction data frame either the naive one (out) from procSample or the EM fit (cncf) from emcncf.
dipLogR	the log-ratio value corresponding to the diploid state.
nfrac	a segment is shown if the proportion of loci and het SNPs (num.mark and nhet) nfrac. Default is 0.01.

Details

This is a diagnostic plot to check how well the copy number fits work. The estimated segment summaries are plotted as circles where the size of the circle increases with the number of loci in the segment. The expected value for various integer copy number states are drawn as curves for purity ranging from 0 to 0.95. For a good fit, the segment summaries should be close to one of the lines.

mskcc/facets documentation built on Oct. 15, 2021, 3:12 p.m.