generateKmers {transite} | R Documentation |
Counts occurrences of k-mers of length k
in the given set of
sequences. Corrects for homopolymeric stretches.
generateKmers(sequences, k)
sequences |
character vector of DNA or RNA sequences |
k |
length of k-mer, either |
Returns a named numeric vector, where the elements are k-mer counts and the names are DNA k-mers.
generateKmers
always returns DNA k-mers, even if
sequences
contains RNA sequences.
RNA sequences are internally converted to DNA sequences. It is not
allowed to mix DNA and
RNA sequences.
Other k-mer functions: calculateKmerEnrichment
,
checkKmers
,
computeKmerEnrichment
,
drawVolcanoPlot
,
empiricalEnrichmentMeanCDF
,
generatePermutedEnrichments
,
homopolymerCorrection
,
permTestGeometricMean
,
runKmerSPMA
, runKmerTSMA
# count hexamers in set of RNA sequences rna.sequences <- c( "CAACAGCCUUAAUU", "CAGUCAAGACUCC", "CUUUGGGGAAU", "UCAUUUUAUUAAA", "AAUUGGUGUCUGGAUACUUCCCUGUACAU", "AUCAAAUUA", "AGAU", "GACACUUAAAGAUCCU", "UAGCAUUAACUUAAUG", "AUGGA", "GAAGAGUGCUCA", "AUAGAC", "AGUUC", "CCAGUAA", "UUAUUUA", "AUCCUUUACA", "UUUUUUU", "UUUCAUCAUU", "CCACACAC", "CUCAUUGGAG", "ACUUUGGGACA", "CAGGUCAGCA" ) hexamer.counts <- generateKmers(rna.sequences, 6) # count heptamers in set of DNA sequences dna.sequences <- c( "CAACAGCCTTAATT", "CAGTCAAGACTCC", "CTTTGGGGAAT", "TCATTTTATTAAA", "AATTGGTGTCTGGATACTTCCCTGTACAT", "ATCAAATTA", "AGAT", "GACACTTAAAGATCCT", "TAGCATTAACTTAATG", "ATGGA", "GAAGAGTGCTCA", "ATAGAC", "AGTTC", "CCAGTAA", "TTATTTA", "ATCCTTTACA", "TTTTTTT", "TTTCATCATT", "CCACACAC", "CTCATTGGAG", "ACTTTGGGACA", "CAGGTCAGCA" ) hexamer.counts <- generateKmers(dna.sequences, 7)