addPrimingWeights {Genominator} | R Documentation

## Adding priming weights to an AlignedRead object.

### Description

This function adds priming weights to an AlignedRead object.

### Usage

    addPrimingWeights(aln, weights = NULL, overwrite = FALSE, ...)

### Arguments

`aln` | An object of class `AlignedRead`.
`weights` | A vector of weights as produced by `computePrimingWeights`.
`overwrite` | A logical, will a `weights` entry in the `alignData` of the `aln` argument be overwritten?
`...` | These arguments are passed to `computePrimingWeights` and are only used if `weights` are `NULL`.

### Details

If the weights are not supplied, the weights are calculated using the `aln` object itself.

### Value

An object of class `AlignedRead` with a `weights` component in its `alignData` slot.

### 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

`computePrimingWeights` and the extended example in the 'Working with ShortRead' vignette.

### Examples

    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)
    }

[Package Genominator version 1.40.0 Index]