binnedAFs {h5vc} | R Documentation |
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
binnedAFs(data, sampledata, normalise = TRUE, binWidth = 0.05, minCov = 10, minCount = 2)
data |
A |
sampledata |
Sample metadata describing the cohort, can be extracted from an HDF5 tally file using the |
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. |
A matrix of AF bins times samples.
Paul Theodor Pyl
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]]