cnNeutralDepthFromHetSites: cnNeutralDepthFromHetSites

In chrisamiller/copyCat: Find regions of genomic copy number loss and gain from short reads

Description

examines heterozygous SNP positions in fixed windows to identify copy-number neutral regions. Finds the median read depth in these regions and uses it as the baseline for copy number estimation.

Usage

  cnNeutralDepthFromHetSites(rdo, samtoolsFile, snpBinSize, peakWiggle=3, minimumDepth=20, maximumDepth=100, plot=FALSE)

Arguments

rdo	a readDepth object filled with read counts
samtoolsFile	the path to a file containing the output of running 'samtools mpileup' on the bam file
snpBinSize	the size of the window to use for counting het sites and estimating peaks. Default of 1MB should be reasonable for most human genomes.
peakWiggle	The amount of "wiggle" allowed in classifying peaks. For example, if peak wiggle is set to 5, a peak at 45 cn-neutral, while a peak at 44
minimumDepth	The minimum depth of coverage needed to consider a het snp site. Prevents sampling error due to low coverage.
maximumDepth	The maximum depth of coverage allowable at a het snp site. Prevents consideration of sites with aberrantly high depth due to mapping artifacts.
plot	Whether to generate density plots of each peak for visual review. Places these in the output directory, under plots/vafPlots

Value

a number that represents the median depth of coverage in copy-number neutral sites.

Examples

  # tumorSamtoolsFile = "samtools.mpileup.output" 
  # rdo@params$med = cnNeutralDepthFromHetSites(rdo, tumorSamtoolsFile,
  #                      snpBinSize=1000000, plot=TRUE)

chrisamiller/copyCat documentation built on July 20, 2021, 12:59 a.m.