resultsProcess: Processing peeling results

In DiNAMIC.Duo: Finding Recurrent DNA Copy Number Alterations and Differences

Processing peeling results

Description

Processing peeling results

Usage

resultsProcess(peel.results, posDT)

Arguments

peel.results	peeling results
posDT	a data frame containing gene annotation information; a list component created by dataPrep.

Details

The peelingOneIterate function identifies (i) multiple loci across the genome where copy number gains are losses, and (ii) regions around those loci that also exhibit copy number changes. Similarly, peelingTwoIterate identifies loci and surrounding regions that harbor copy number differences. The output of either peelingOneIterate or peelingTwoIterate is processed to produce a tab-delimited text file that provides a summary of the peeling results. Each column corresponds to a peeled locus, and the column contains the genomic location of the locus, the start and end positions of the surrounding peeled region, the mean copy number value (one matrix X) or difference of mean copy number values (two matrices X and Y), the cyclic shift-based p-value, and the names of the genes in the peeled region (in alphabetical order).

Value

processed peeling results with a list of genes corresponding to each peeled region

See Also

dataPrep

DiNAMIC.Duo documentation built on March 7, 2023, 8:38 p.m.