generate_iupac_by_kmers: Generates IUPAC code for a character vector of _k_-mers

In transite: RNA-binding protein motif analysis

Description

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

Usage

generate_iupac_by_kmers(kmers, code = NULL)

Arguments

kmers	character vector of k-mers
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_matrix(), generate_kmers_from_iupac(), get_motif_by_id(), get_motif_by_rbp(), get_motifs_meta_info(), get_motifs(), get_ppm(), init_iupac_lookup_table(), set_motifs()

Examples

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

transite documentation built on Nov. 8, 2020, 5:27 p.m.