generateIUPACByMatrix {transite} | R Documentation |
Generates a compact logo of a motif based on IUPAC codes given by a position weight matrix
generateIUPACByMatrix(matrix, threshold = 0.215, code = NULL)
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
|
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 |
the IUPAC string of the binding site
http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
Other motif functions: generateIUPACByKmers
,
generateKmersFromIUPAC
,
getMotifById
, getMotifByRBP
,
getMotifs
, getPPM
,
initIUPAClookupTable
,
motifsMetaInfo
, setMotifs
generateIUPACByMatrix(motifMatrix(getMotifById("M178_0.6")[[1]]))