flankingSequence: Get flanking sequences of a position.

In omarwagih/rmimp: Predicting the impact of mutations on kinase-substrate phosphorylation

Description

This function obtains the flanking sequence at one or more position. Out of bound indices are replaced by a blank character.

Usage

flankingSequence(seqs, inds, flank = 7, empty_char = "-")

Arguments

seqs	Character vector of sequences. If only one sequence is provided, indices from inds are assumed to all be from the same sequence.
inds	Numerical vector of positions corresponding to the sequences provided in seqs.
flank	Value indicating the number of characters to extract, before and after an index
empty_char	Character used to replace out of bound flanking sequences

Examples

# One sequence and one index. Central character is 'B'
flankingSequence(seqs='ABC', inds=2, flank=1)
# An example showing the use of empty.char 
flankingSequence(seqs='ABC', inds=2, flank=5)
# An example with multiple sequences and indices
flankingSequence(seqs=c('ABC', 'XYZ'), inds=c(2, 1), flank=1)

omarwagih/rmimp documentation built on May 18, 2020, 3:11 p.m.