findMatchesByChromosomalRegion: Find Motif Matches by Chromosomal Region

In trena: Fit transcriptional regulatory networks using gene expression, priors, machine learning

Description

Given a MotifMatcher object, a table of chromosomal regions, and a minimum match percentage, pull out a list containing a data frame of the motifs in those regions and a character vector of their associated transcription factors.

Usage

## S4 method for signature 'MotifMatcher'
findMatchesByChromosomalRegion(
  obj,
  tbl.regions,
  pwmMatchMinimumAsPercentage,
  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".
pwmMatchMinimumAsPercentage	A percentage (0-100) used as a cutoff for what constitutes a motif match
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

A list containing a data frame of the motifs in the given regions and a character vector of their associated transcription factors

Examples

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

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

## End(Not run)

trena documentation built on Nov. 15, 2020, 2:07 a.m.