dot-view_gr_by_window_sample: view GRanges with score at specified window size by sampling...

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

Description

view GRanges with score at specified window size by sampling values

Usage

.view_gr_by_window_sample(score_gr, query_gr, window_size,
  anchor = c("center", "center_unstranded", "left",
  "left_unstranded")[1])

Arguments

score_gr	GRanges with score mcol
query_gr	GRanges that was used to fecth score_gr
window_size	ineger. desired window size.
anchor	character, anchoring method. one of "center", "center_unstranded", "left", "left_unstranded"

Value

data.table of scores stored in y value sample every window_size

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

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