count_homopolymer_corrected_kmers {transite} | R Documentation

## Correction for Homopolymeric Stretches

### Description

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

### Usage

    count_homopolymer_corrected_kmers(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: `calculate_kmer_enrichment()`, `check_kmers()`, `compute_kmer_enrichment()`, `draw_volcano_plot()`, `estimate_significance_core()`, `estimate_significance()`, `generate_kmers()`, `generate_permuted_enrichments()`, `run_kmer_spma()`, `run_kmer_tsma()`

[Package transite version 1.8.0 Index]