computePrimingWeights: Compute weights to correct for random hexamer priming.

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

Description

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

Usage

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

Arguments

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.

Value

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.

Author(s)

Kasper Daniel Hansen khansen@jhsph.edu.

References

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

See Also

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

Examples

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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)
}


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