clean_granges_for_cesa: clean_granges_for_cesa

In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

clean_granges_for_cesa

Description

Tries to format an input GRanges object to be compatible with a CESAnalysis reference genome. Optionally, also applies padding to start and end positions of ranges, stopping at chromosome ends. Either stops with an error or returns a clean granges object.

Usage

clean_granges_for_cesa(
  cesa = NULL,
  gr = NULL,
  padding = 0,
  refset_env = NULL,
  reduce_sort_strip = TRUE
)

Arguments

cesa	CESAnalysis; required unless refset_env is supplied directly.
gr	GRanges object
padding	How many bases to expand start and end of each position
refset_env	A reference data set environment. Required if cesa is not specified.
reduce_sort_strip	Unstrands and calls reduce(gr) which also drops all metadata columns, and then sorts the final gr. Default TRUE; use FALSE to preserve original gr structure.

Townsend-Lab-Yale/cancereffectsizeR documentation built on April 28, 2024, 6:14 p.m.