callVariantsFisher: Paired variant calling using fisher tests

In h5vc: Managing alignment tallies using a hdf5 backend

Description

This function implements a simple paired variant calling strategy based on the fisher test

Usage

callVariantsPairedFisher(data, sampledata, pValCutOff = 0.05, minCoverage = 5, mergeDels = TRUE, mergeAggregator = mean)

Arguments

data	A list with elements Counts (a 4d integer array of size [1:12, 1:2, 1:k, 1:n]), Coverage (a 3d integer array of size [1:2, 1:k, 1:n]), Reference (a 1d integer vector of size [1:n]) – see Details.
sampledata	A data.frame with k rows (one for each sample) and columns Type, Column and (Group or Patient). The tally file should contain this information as a group attribute, see getSampleData for an example.
pValCutOff	Maximum allowed p-Value for the fisher test on contingency matrix matrix(c(caseCounts, caseCoverage, controlCounts, controlCoverage), nrow=2).
minCoverage	Required coverage in both sample for a call to be made
mergeDels	Boolean flag specifying whether adjacent deletions should be merged
mergeAggregator	Which function to use for aggregating the values associated with adjacent deletions that are being merged

Details

data is a list which has to at least contain the Counts, Coverages and Reference datasets. This list will usually be generated by a call to the h5dapply function in which the tally file, chromosome, datasets and regions within the datasets would be specified. See h5dapply for specifics.

callVariantsPairedFisher implements a simple pairwise variant callign approach based on using the fisher.test on the following contingency matrix:

caseSupport	caseCoverage - caseSupport
conttrolSupport	controlCoverage - controlSupport

The results are filtered by pValCutOff and minCoverage.

Value

The return value is a data.frame with the following slots:

Chrom	The chromosome the potential variant is on
Start	The starting position of the variant
End	The end position of the variant
Sample	The Case sample in which the variant was observed
refAllele	The reference allele
altAllele	The alternate allele
caseCount	Support for the variant in the Case sample
caseCoverage	Coverage of the variant position in the Case sample
controlCount	Support for the variant in the Control sample
controlCoverage	Coverage of the variant position in the Control sample
pValue	The p.value of the fisher.test

Author(s)

Paul Pyl

Examples

library(h5vc) # loading library
tallyFile <- system.file( "extdata", "example.tally.hfs5", package = "h5vcData" )
sampleData <- getSampleData( tallyFile, "/ExampleStudy/16" )
position <- 29979629
windowsize <- 2000
vars <- h5dapply( # Calling Variants
  filename = tallyFile,
  group = "/ExampleStudy/16",
  blocksize = 1000,
  FUN = callVariantsPairedFisher,
  sampledata = sampleData,
  pValCutOff = 0.1,
  names = c("Coverages", "Counts", "Reference"),
  range = c(position - windowsize, position + windowsize),
  verbose = TRUE
)
vars <- do.call(rbind, vars)
vars

h5vc documentation built on Nov. 8, 2020, 4:56 p.m.