getSequence,MotifMatcher-method {trena} | R 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)

[Package trena version 1.12.1 Index]