computePrimingWeights {Genominator} | R Documentation |
This function computes weights used to correct for random hexamer priming, as per the reference.
computePrimingWeights(aln, biasedIndex = 1:2, unbiasedIndex = 24:29, weightsLength = 7L, returnSep = FALSE)
aln |
An object of class |
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) }