# Compute weights to correct for random hexamer priming.

### Description

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

### Usage

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

### Arguments

`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. |

### 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

1 2 3 4 5 6 7 8 | ```
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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