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

View source: R/primingWeights.R

This function adds priming weights to an AlignedRead object.

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

`aln` |
An object of class |

`weights` |
A vector of weights as produced by |

`overwrite` |
A logical, will a |

`...` |
These arguments are passed to |

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.

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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