generate_iupac_by_matrix: Generates IUPAC code for motif matrix

In kkrismer/transite: RNA-binding protein motif analysis

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

generate_iupac_by_matrix(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 init_iupac_lookup_table, 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: generate_iupac_by_kmers(), generate_kmers_from_iupac(), get_motif_by_id(), get_motif_by_rbp(), get_motifs(), get_motifs_meta_info(), get_ppm(), init_iupac_lookup_table(), set_motifs()

Examples

generate_iupac_by_matrix(get_motif_matrix(get_motif_by_id("M178_0.6")[[1]]))

kkrismer/transite documentation built on Feb. 9, 2024, 3:23 a.m.