generateIUPACByMatrix {transite}R Documentation

Generates IUPAC code for motif matrix

Description

Generates a compact logo of a motif based on IUPAC codes given by a position weight matrix

Usage

generateIUPACByMatrix(matrix, threshold = 0.215, code = NULL)

Arguments

matrix

the position probability matrix of an RNA-binding protein

threshold

the threshold probability (nucleotides with lower probabilities are ignored)

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: generateIUPACByKmers, generateKmersFromIUPAC, getMotifById, getMotifByRBP, getMotifs, getPPM, initIUPAClookupTable, motifsMetaInfo, setMotifs

Examples

generateIUPACByMatrix(motifMatrix(getMotifById("M178_0.6")[[1]]))

[Package transite version 1.2.1 Index]