binnedAFs {h5vc}

R Documentation

Estimate allelic frequency distributions in bins along the genome

Description

This function is used to give estimates of the ditribution of observed allelic freuqencies in a regions of the genome, use in conjunction with h5dapply

Usage

binnedAFs(data, sampledata, normalise = TRUE, binWidth = 0.05, minCov = 10, minCount = 2)

Arguments

data	A list object returned by a call to h5dapply or h5readBlock.
sampledata	Sample metadata describing the cohort, can be extracted from an HDF5 tally file using the getSampleData function.
normalise	Boolean flag to specify whether the counts or percentages of observed allelic frequencies should be returned.
binWidth	Width of bins in allelic frequency space, defaults to 0.05.
minCov	Minimum required coverage for a position to be considered.
minCount	Minimum required number of mismatches for a position to be considered.

Value

A matrix of AF bins times samples.

Author(s)

Paul Theodor Pyl

Examples

library(h5vc)
tallyFile <- system.file( "extdata", "example.tally.hfs5", package = "h5vcData" )
sampleData <- getSampleData( tallyFile, "/ExampleStudy/16" )
afs <- h5dapply(
  filename = tallyFile,
  group = "/ExampleStudy/16",
  names = c("Counts", "Coverages"),
  range = c(29e6, 29.05e6),
  blocksize = 1e4,
  FUN = binnedAFs,
  sampledata = sampleData
)
afs[[3]]

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