count_homopolymer_corrected_kmers: Correction for Homopolymeric Stretches

In kkrismer/transite: RNA-binding protein motif analysis

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(), create_kmer_origin_list(), draw_volcano_plot(), estimate_significance(), estimate_significance_core(), generate_kmers(), generate_permuted_enrichments(), run_kmer_spma(), run_kmer_tsma()

kkrismer/transite documentation built on July 13, 2024, 8:01 a.m.