wigsToRangedData {HMMcopy} | R Documentation

## Parsing and sorting of uncorrected read and sequence information files

### Description

Loads WIG files for readcount, GC, and mappability data for non-overlapping windows of fixed length (i.e. bins), and returns a structure ready to used for readcount correction. See Details for specifics about file assumptions.

### Usage

    wigsToRangedData(readfile, gcfile, mapfile, verbose = FALSE)

### Arguments

`readfile` | Pathname to WIG file containing readcounts per bin.
`gcfile` | Pathname to WIG file containing GC content per bin.
`mapfile` | Pathname to WIG file containing average mappability per bin.
`verbose` | Set to TRUE if messages are desired

### Details

The number of lines in the three input files are expected to be identical, although the order and names of chromsomes in the file need not be identical. Chromosome lengths are required to be identical and unique, and if the latter is not true, the order of the chromosomes must then be identical.

At present, these three WIG files are expected to be generated by external programs, namely those from the HMMcopy suite (see See Also), rather than by existing R packages out of space and memory considerations when working with high coverage full genome samples.

### Value

A `RangedData` object, where each row entry represents a bin, with the three values from the input as columns named reads, gc, and map.

### Author(s)

Daniel Lai

### References

correctedReadcount Suite

  TBA

WIG

  http://genome.ucsc.edu/goldenPath/help/wiggle.html

### See Also

`correctReadcount`, to correct the readcounts in the resultant value.

### Examples

    rfile <- system.file("extdata", "tumour.wig", package = "HMMcopy")
    gfile <- system.file("extdata", "gc.wig", package = "HMMcopy")
    mfile <- system.file("extdata", "map.wig", package = "HMMcopy")

    uncorrected_reads <- wigsToRangedData(rfile, gfile, mfile)

[Package HMMcopy version 1.22.0 Index]