Coverage {h5vc} | R Documentation

## 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

### Details

Explanations:

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

### 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.

### Author(s)

Paul Pyl

### 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)

[Package h5vc version 2.14.0 Index]