rosy: Run rosy.

In mal2017/rosy: Super enhancers in R.

Description

Run rosy.

Usage

rosy(regions, reads, paired = F, colData, txdb = NULL,
  stitchDist = 12500, se_cutoff = "optimize", exclude = NULL)

## S4 method for signature 'GRanges,character,ANY,data.frame'
rosy(regions, reads,
  paired = F, colData, txdb = NULL, stitchDist = 12500,
  se_cutoff = "optimize", exclude = NULL)

Arguments

regions	GRanges, list of GRanges, GRangesList, path to file, or list of paths.
reads	Object or path to file containing reads, or list.
paired	Logical indicating paired-end reads or list.
colData	dataframe with sample information.
stitchDist	Enhancer stitching distance.
se_cutoff	Either 'optimize' or an integer indicating the top n enhancers to consider as SE.
exclude	GRanges of regions to exclude

mal2017/rosy documentation built on May 17, 2019, 3:12 a.m.