getSequenceContext {YAPSA}R Documentation

Extracts the sequence context up and downstream of a nucleotide position

Description

Extracts the sequence context up and downstream of a nucleotide position

Usage

getSequenceContext(position, chr, offsetL = 10, offsetR = 50)

Arguments

position

Start position of the considered INDEL

chr

Chromosome of the considered INDEL

offsetL

Number of nucleotides downstream of position

offsetR

Number of nucleotides upstream of position

Value

Returns a character string containing the defined seqeunce context

Examples

library(Biostrings)
library(BSgenome.Hsapiens.UCSC.hg19)

sequence_context <- getSequenceContext(position = 123456789, chr = "chr12",
                                       offsetL= 10, offsetR=50)
sequence_context
[Package YAPSA version 1.13.4 Index]