computePrimingWeights: Compute weights to correct for random hexamer priming.
In Genominator: Analyze, manage and store genomic data

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

This function computes weights used to correct for random hexamer priming, as per the reference.

1 2	computePrimingWeights(aln, biasedIndex = 1:2, unbiasedIndex = 24:29, weightsLength = 7L, returnSep = FALSE)

`aln`	An object of class `AlignedRead`.
`biasedIndex`	A vector of start positions for the biased k-mers.
`unbiasedIndex`	A vector of start positions for the unbiased k-mers.
`weightsLength`	The length of the k-mers.
`returnSep`	A logical indicating whether the numerator and denominator of the weights should be return or the weights themselves.

If returnSep = FALSE a named vector of weights. Otherwise a list with two elements giving the numerator (p_unbiased) and the denominator (p_biased) of the weights.

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

addPrimingWeights 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)
}