Extract the sequence context around positions of interest

This function will extract a sequence context of sequenceContextWidth bases around the center of the regions defined in x from sequenceReference.

Usage

extractSeqContext(x, sequenceContextWidth, sequenceReference)

Arguments

x: A GRanges object defining the regions of interest. Alternatively, a RangedSummarizedExperiment object from which regions can be extracted using rowRanges. The extracted sequences will correspond to the regions defined as resize(x, width = sequenceContextWidth, fix = "center".
sequenceContextWidth: A numeric scalar giving the width of the sequence context to be extracted from the reference (sequenceReference argument). This must be an odd number so that the sequence can be centered on the modified base. If sequenceContextWidth = 0 (the default), no sequence context will be extracted.
sequenceReference: A DNAStringSet object, a BSgenome object, or a character scalar giving the path to a fasta formatted file with reference sequences. If a BSgenome object is provided, it will be internally converted to a DNAStringSet object, since the latter allows for faster sequence retrieval.

Value

A DNAStringSet object of the same length as x with extracted sequence context. All elements are guaranteed to have identical length (if the sequence context extends to before the start or beyond the end of a reference sequence, it will be padded with 'N' bases.

Author

Michael Stadler

Examples

# file with sequence in fasta format of length 6957060
reffile <- system.file("extdata", "reference.fa.gz", package = "footprintR")

# define some regions at the end of the reference sequence
regions <- GenomicRanges::GRanges(
    "chr1", IRanges::IRanges(start = 6957060 - c(4, 2, 0),
    width = 1, names = c("a", "b", "c")))

# extract sequence context (note the padding with N's)
extractSeqContext(regions, 7, reffile)
#> DNAStringSet object of length 3:
#>     width seq                                               names               
#> [1]     7 AAAGGGG                                           a
#> [2]     7 AGGGGAN                                           b
#> [3]     7 GGGANNN                                           c