procSample: Process a sample

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

Description

Processes the output from preProcSample for given cval and min.nhet

Usage

  procSample(x, cval=150, min.nhet=15, dipLogR=NULL)

Arguments

x	the output from preProcSample; should contain seg.tree and jointseg
cval	critical value for segmentation
min.nhet	minimum number of heterozygote snps in a segment used for bivariate t-statistic during clustering of segments
dipLogR	diploid level obtained from a fit, typically using a higher cval, can be used with lower cval to recover focal changes

Details

The minor copy number lcn may not be estimated with confidence when a segment has fewer than min.nhet heterozygous SNPs and hence will return NA. If there are too few heterozygous SNPs in a segment then mafR and mafR.clust can be NA.

Value

A list consisting of two elements:

jointseg	The data that were segmented. Only the loci that were sampled within a snp.nbhd are present
out	data frame of segment summaries pre and post clustering of segments. The columns are: chrom the chromosome to which the segment belongs; seg the segment number; num.mark the number of SNPs in the segment; nhet the number of SNPs that are deemed heterozygous; cnlr.median the median log-ratio of the segment; mafR the log-odds-ratio summary for the segment; segclust the segment cluster to which segment belongs; cnlr.median.clust the median log-ratio of the segment cluster; mafR.clust the log-odds-ratio summary for the segment cluster; cf the cellular fraction of the segment; tcn the total copy number of the segment; lcn the minor copy number of the segment.
dipLogR	specified or obtained from data
...	other output when findDiploidLogR is used

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