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 1.2.0 Index]