getSequence: Retrieve the Sequence for a Set of Regions

getSequence,MotifMatcher-methodR Documentation

Retrieve the Sequence for a Set of Regions

Description

Given a MotifMatcher object, a table of chromosomal regions, and an optional set of variants, return the sequences as a new column of the table.

Usage

## S4 method for signature 'MotifMatcher'
getSequence(obj, tbl.regions, variants = NA_character_)

Arguments

obj

An object of class MotifMatcher

tbl.regions

A data frame where each row contains a chromosomal region with the fields "chrom", "start", and "end".

variants

A character containing variants to use for the matching (default = NA_character_) The variants should either have the same number of entries as rows in the tbl.regions, or they should not be supplied.

Value

The tbl.regions data frame with an added column containing the sequence for each entry

Examples

## Not run: 
# Retrieve the sequences for the rs13384219 neighborhood
library(MotifDb)
motifMatcher <- MotifMatcher(genomeName="hg38",
pfms = as.list(query(query(MotifDb, "sapiens"), "jaspar2016")))
tbl.regions <- data.frame(chrom="chr2", start=57907313, end=57907333, stringsAsFactors=FALSE)
x <- findMatchesByChromosomalRegion(motifMatcher, tbl.regions, pwmMatchMinimumAsPercentage=92)

# Retrieve the sequences, but now include a variant
x.mut <- findMatchesByChromosomalRegion(motifMatcher, tbl.regions,
pwmMatchMinimumAsPercentage=92, "rs13384219")

## End(Not run)

PriceLab/TReNA documentation built on March 21, 2023, 1:57 p.m.