prepare_fetch_GRanges: prepares GRanges for windowed fetching.

In seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

Description

output GRanges parallels input with consistent width evenly divisible by win_size. Has warning if GRanges needed resizing, otherwise no warning and input GRanges is returned unchanged.

Usage

prepare_fetch_GRanges(
  qgr,
  win_size,
  min_quantile = 0.75,
  target_size = NULL,
  skip_centerFix = FALSE
)

Arguments

qgr	GRanges to prepare
win_size	numeric window size for fetch
min_quantile	numeric [0,1], lowest possible quantile value. Only relevant if target_size is not specified.
target_size	numeric final width of qgr if known. Default of NULL leads to quantile based determination of target_size.
skip_centerFix	boolean, if FALSE (default) all regions will be resized GenomicRanges::resize(x, w, fix = "center") to a uniform size based on min_quantile to a width divisible by win_size.

Value

GRanges, either identical to qgr or with suitable consistent width applied.

Examples

qgr = prepare_fetch_GRanges(CTCF_in_10a_overlaps_gr, win_size = 50)
#no warning if qgr is already valid for windowed fetching
prepare_fetch_GRanges(qgr, win_size = 50)

seqsetvis documentation built on Nov. 8, 2020, 5:57 p.m.