generate_kmers_from_iupac: Generates all _k_-mers for IUPAC string

In kkrismer/transite: RNA-binding protein motif analysis

Generates all k-mers for IUPAC string

Description

Generates all possible k-mers for a given IUPAC string.

Usage

generate_kmers_from_iupac(iupac, k)

Arguments

iupac	IUPAC string
k	length of k-mer, 6 (hexamers) or 7 (heptamers)

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

list of k-mers

References

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

See Also

Other motif functions: generate_iupac_by_kmers(), generate_iupac_by_matrix(), get_motif_by_id(), get_motif_by_rbp(), get_motifs(), get_motifs_meta_info(), get_ppm(), init_iupac_lookup_table(), set_motifs()

Examples

generate_kmers_from_iupac(get_iupac(get_motif_by_id("M178_0.6")[[1]]), k = 6)

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