extra_motif_seq: Scanning specific motifs in the transcripts.

In cma2015/PEA-m5C: An integrated R toolkit for plant m5C analysis.

Description

For a given motif, all transcript sequences will be scanned according to the user-specific flanking sequence length (upstream/downstream), then the fixed length of sequences centered on motif will be returned.

Usage

extra_motif_seq(input_seq_dir,text='c',up=5,end=5)

Arguments

input_seq_dir	A string character, representing the directory of the sequence in FASTA format.
text	A string character, which specifies the motif to be searched.
up	A integer number, the length of upstream sequence to be extracted.
end	A integer number, the length of downstream sequence to be extracted.

Value

A list of sequences around motif.

Author(s)

Jie Song, Jingjing Zhai, Chuang Ma

Examples

aaa <- extra_motif_seq(input_seq_dir = paste0(system.file(package = "PEAm5c"),"/data/cdna.fa"),up = 5)
aaa

cma2015/PEA-m5C documentation built on May 17, 2019, 8:05 a.m.