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Trim sequences to a specified width around the summit

Source: R/trim_seqs.R
trim_seqs.Rd

Trim sequences to a specified width around the summit

Usage

trim_seqs(peaks, peak_width, genome_build, respect_bounds = TRUE)

Arguments

peaks

A GRanges object created using read_peak_file().

peak_width

Total expected width of the peak.

genome_build

The genome build that the peak sequences should be derived from.

respect_bounds

Logical indicating whether the peak width should be respected when trimming sequences. (default = TRUE) If TRUE, the trimmed sequences will not extend beyond the peak boundaries.

Value

A GRanges object with the trimmed sequences. The sequences are guaranteed to not exceed the peak width + 1 (peak width + the summit base).

Examples

data("CTCF_TIP_peaks", package = "MotifPeeker")
peaks <- CTCF_TIP_peaks
genome_build <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38

trimmed_seqs <- trim_seqs(peaks, peak_width = 100,
                         genome_build = genome_build)
summary(GenomicRanges::width(trimmed_seqs))
#>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
#>    59.0   101.0   101.0    98.5   101.0   101.0