homopolymerCorrection {transite} | R Documentation

## Correction for Homopolymeric Stretches

### Description

Counts all non-overlapping instances of k-mers in a given set of sequences.

### Usage

    homopolymerCorrection(sequences, k, kmers, is.rna = FALSE)

### Arguments

`sequences` | character vector of DNA or RNA sequences
`k` | length of k-mer, either `6` for hexamers or `7` for heptamers
`kmers` | column sums of return value of `Biostrings::oligonucleotideFrequency(sequences)`
`is.rna` | if `sequences` are RNA sequences, this flag needs to be set

### Value

Returns a named numeric vector, where the elements are k-mer counts and the names are k-mers.

### See Also

Other k-mer functions: `calculateKmerEnrichment`, `checkKmers`, `computeKmerEnrichment`, `drawVolcanoPlot`, `empiricalEnrichmentMeanCDF`, `generateKmers`, `generatePermutedEnrichments`, `permTestGeometricMean`, `runKmerSPMA`, `runKmerTSMA`

[Package transite version 1.2.1 Index]