dot-shift_anchor: applies an anchor which controls x coordinate system 1)...

In jrboyd/peakrefine: Peak Refinement Metric Gathering and Evalutation by Motif Enrichment

Description

applies an anchor which controls x coordinate system 1) should 0 on the x-axis be on the left or in the center? 2) should - strand signal be flipped?

Usage

.shift_anchor(score_dt, window_size, anchor)

Arguments

score_dt	data.table, mandatory columns are start, end, and id. strand is also mandatory if not anchoring *_unstranded.
window_size	the window size at which score was calculated/retrieved
anchor	character, one of center, center_unstranded, left, left_unstranded.

Value

data.table with x added according to anchor

Examples

library(GenomicRanges)
bam_file = system.file("extdata", "MCF10A_CTCF.random5.bam", package = "peakrefine")
bam_input = system.file("extdata", "MCF10A_input.random5.bam", package = "peakrefine")
np = system.file("extdata", "MCF10A_CTCF.random5.narrowPeak", package = "peakrefine")
qgr = rtracklayer::import(np, format = "narrowPeak")
strand(qgr) = c("+", "-", "-", "+", "-")

reads_dt = peakrefine:::.fetch_bam_stranded(bam_file, qgr)
ext_cov = GenomicRanges::coverage(GenomicRanges::split(
    GenomicRanges::GRanges(reads_dt[strand == "+"]), reads_dt$which_label))
score_gr = GenomicRanges::GRanges(ext_cov)
bam_dt = peakrefine:::.view_gr_by_window_sample(score_gr, qgr, 1,
                                 anchor = "center_unstranded")
peakrefine:::.shift_anchor(bam_dt, 1, "center_unstranded")

jrboyd/peakrefine documentation built on July 30, 2020, 7:13 p.m.