findMatchesByChromosomalRegion,MotifMatcher-method {trena} | R Documentation

## Find Motif Matches by Chromosomal Region

### 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)

[Package trena version 1.12.1 Index]