getSequenceContext: Extracts the sequence context up and downstream of a...
In slw287r/yapsa: Yet Another Package for Signature Analysis

Description Usage Arguments Value Examples

Extracts the sequence context up and downstream of a nucleotide position

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

`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`

Returns a character string containing the defined seqeunce context

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

sequence_context <- getSequenceContext(position = 123456789, chr = "chr12",
                                       offsetL= 10, offsetR=50)
sequence_context