generateIUPACByKmers {transite}R Documentation

Generates IUPAC code for a character vector of k-mers

Description

Generates a compact logo of a motif based on IUPAC codes given by a character vector of k-mers

Usage

generateIUPACByKmers(kmers, code = NULL)

Arguments

kmers

character vector of k-mers

code

if IUPAC code table has already been initialized by initIUPAClookupTable, it can be specified here

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

the IUPAC string of the binding site

References

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

See Also

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

Examples

generateIUPACByKmers(c("AACCAA", "AACCGG", "CACCGA"))

[Package transite version 1.2.0 Index]