truncate_seq: truncate_seq function

In wokai/spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

Description

truncateSeqs amino acid sequences at positions depicted by '*' (stop-codon).

Usage

truncate_seq(seq,pos,id,rme=TRUE,trunc=42L)

Arguments

seq	Character. Amino-acid sequences which are to be truncated.
pos	Numeric. Points to an amino-acid inside the sequence.
id	Numeric. An identifier which is copied to the result table.
rme	Logical. Empty sequences are removed when set to TRUE.
trunc	Integer. ASCII code for character at which truncation should occur. Default value is 42='*' (stop-codon).

Details

The function truncateSeqs the contained amino acid sequences. When the stop-codon is found on the left side of position, the function returns an empty sequence for that site. The position values for these records are also set to 0.

Value

data.frame

Author(s)

Wolfgang Kaisers

Examples

truncate_seq(seq="ARPX*QR",pos=3)

wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.