h5vc (version 2.6.3)

Coverage: Coverage analysis

Description

Functions to do analyses based on coverage

Usage

binnedCoverage( data, sampledata, gccount = FALSE )

Arguments

data

A list with element Coverage (a 3d integer array of size [1:2, 1:k, 1:n])

sampledata

A data.frame with k rows (one for each sample) and columns Type, Column and (SampleGroup or Patient). The tally file should contain this information as a group attribute, see getSampleData for an example.

gccount

Boolean flag to specify whether the gc count of the bin should be reported as well, Reference must be a slot in the data object

Value

• Returns a data.frame with columns containing the coverage with the current bin for all samples provided in sampledata. The binsize is determined by the blocksize argument given to h5dapply when this function is run directly on a tally file.

Details

Explanations:

This computes the per sample coverage in a given bin (determined by the width of data). This feature is not implemented yet!

Examples

# loading library and example data
  library(h5vc)
  tallyFile <- system.file( "extdata", "example.tally.hfs5", package = "h5vcData" )
  sampleData <- getSampleData( tallyFile, "/ExampleStudy/22" )
  data <- h5dapply( # extractting coverage binned at 1000 bases
    filename = tallyFile,
    group = "/ExampleStudy/22",
    blocksize = 1000,
    FUN = binnedCoverage,
    sampledata = sampleData,
    gccount = TRUE,
    names = c( "Coverages", "Reference" ),
    range = c(38900000,39000000)
  )
  data <- do.call(rbind, data)
  rownames(data) <- NULL
  head(data)