pileup_gr_list: Pileup reads, fragments, or cuts from a BAM file over target...

In AllenInstitute/lowcat: Low Coverage Accessibility and Transcriptomics

Description

Pileup reads, fragments, or cuts from a BAM file over target GRanges regions.

Usage

pileup_gr_list(gr_list, gr_target, gr_groups = NULL, norm = c("PM",
  "max"), window_size = NULL, window_mode = c("max", "mean", "median"))

Arguments

gr_list	A list of GRanges objects
gr_target	A single GRanges object for the target region to plot.
gr_groups	A vector indicating which group each GRanges object in gr_list belongs to. If NULL, will group all samples into a single track.
norm	Normalization for each group. Currently support is per-million ("PM") and "max".
window_size	Window bin size to use for region down-sampling. If NULL, will not downsample.
window_mode	If using window_size, what value to use for each window. Options are "max","mean", and "median".

Value

list of data.frames, one per group in gr_groups. Each data.frame has pos (position) and val (value) columns.

AllenInstitute/lowcat documentation built on Oct. 30, 2019, 4:45 a.m.