init_iupac_lookup_table: Initializes the IUPAC lookup table

In kkrismer/transite: RNA-binding protein motif analysis

Initializes the IUPAC lookup table

Description

Initializes a hash table that serves as a IUPAC lookup table for the generate_iupac_by_matrix function.

Usage

init_iupac_lookup_table()

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

an environment, the IUPAC lookup hash table

References

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

See Also

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

Examples

generate_iupac_by_matrix(get_motif_matrix(get_motif_by_id("M178_0.6")[[1]]),
  code = init_iupac_lookup_table())

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