generateKmersFromIUPAC {transite}R Documentation

Generates all k-mers for IUPAC string

Description

Generates all possible k-mers for a given IUPAC string.

Usage

generateKmersFromIUPAC(iupac, k)

Arguments

iupac

IUPAC string

k

length of k-mer, 6 (hexamers) or 7 (heptamers)

Details

IUPAC RNA nucleotide code:

A Adenine
C Cytosine
G Guanine
U Uracil
R A or G
Y C or U
S G or C
W A or U
K G or U
M A or C
B C or G or U
D A or G or U
H A or C or U
V A or C or G
N any base

Value

list of k-mers

References

http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html

See Also

Other motif functions: generateIUPACByKmers, generateIUPACByMatrix, getMotifById, getMotifByRBP, getMotifs, getPPM, initIUPAClookupTable, motifsMetaInfo, setMotifs

Examples

generateKmersFromIUPAC(motifIUPAC(getMotifById("M178_0.6")[[1]]), k = 6)

[Package transite version 1.2.0 Index]