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()

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