addPrimingWeights: Adding priming weights to an AlignedRead object.
In Genominator: Analyze, manage and store genomic data

Description Usage Arguments Details Value Author(s) References See Also Examples

This function adds priming weights to an AlignedRead object.

1	addPrimingWeights(aln, weights = NULL, overwrite = FALSE, ...)

`aln`	An object of class `AlignedRead`.
`weights`	A vector of weights as produced by `computePrimingWeights`.
`overwrite`	A logical, will a `weights` entry in the `alignData` of the `aln` argument be overwritten?
`...`	These arguments are passed to `computePrimingWeights` and are only used if `weights` are `NULL`.

If the weights are not supplied, the weights are calculated using the aln object itself.

An object of class AlignedRead with a weights component in its alignData slot.

Kasper Daniel Hansen khansen@jhsph.edu.

Hansen, K. D., Brenner, S. E. and Dudoit, S (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res, doi:10.1093/nar/gkq224

computePrimingWeights and the extended example in the 'Working with ShortRead' vignette.

if(require(ShortRead)) {
  bwt.file <- system.file("extdata", "bowtie", "s_1_aligned_bowtie.txt",
                          package="ShortRead")
  aln <- readAligned(bwt.file, type = "Bowtie")
  weights <- computePrimingWeights(aln, weightsLength = 2L)
  aln <- addPrimingWeights(aln, weights = weights)
  head(alignData(aln)$weights)
}