get_sequence {memes} | R Documentation

## Get sequence from GRanges

### Description

A light wrapper around Biostrings::getSeq to return named DNAStringSets, from input genomic coordinates.

### Usage

    get_sequence(regions, genome, score_column, ...)

### Arguments

`regions` | GRanges, or GRangesList object. Will also accept a data.frame as long as it can be coerced to a GRanges object, or a string in the format: "chr:start-end" (NOTE: use 1-based closed intervals, not BED format 0-based half-open intervals).
`genome` | object of any valid type in 'showMethods(Biostrings::getSeq)'. Commonly a BSgenome object, or fasta file. Used to look up sequences in regions.
`score_column` | optional name of column (in mcols() of 'regions') containing a fasta score that is added to the fasta header of each entry. Used when using [runAme()] in partitioning mode. (default: 'NULL')
`...` | additional arguments passed to Biostrings::getSeq.

### Value

'Biostrings::DNAStringSet' object with names corresponding to genomic coordinates. If input is a list object, output will be a 'Biostrings::BStringSetList' with list names corresponding to input list names.

### Examples

    # using character string as coordinates
    # using BSgenome object for genome
    drosophila.genome <- BSgenome.Dmelanogaster.UCSC.dm6::BSgenome.Dmelanogaster.UCSC.dm6
    get_sequence("chr2L:100-200", drosophila.genome)

    # using GRanges object for coordinates
    data(example_peaks, package = "memes")
    get_sequence(example_peaks, drosophila.genome)

[Package memes version 1.0.4 Index]