getSequence: Retrieve the Sequence for a Set of Regions

In PriceLab/trena-until-01mar2018: Fit transcriptional regulatory networks using gene expression, priors, machine learning

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-until-01mar2018 documentation built on May 25, 2019, 1:22 p.m.