coverage: Coverage analysis
In h5vc: Managing alignment tallies using a hdf5 backend

Description Usage Arguments Details Value Author(s) Examples

Functions to do analyses based on coverage

1	binnedCoverage( data, sampledata, gccount = FALSE )

`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

Explanations:

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

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.

Paul Pyl

  # 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)