asGCT: Dump DNA methylation values, gene-level counts, or whatever...

In RamsinghLab/ozymandias: Tools for region- and process-centric analyses of multiple assay types

Description

Dump DNA methylation values, gene-level counts, or whatever for IGV viewing

Usage

asGCT(x, toTDF = F, assay = 1, group = NULL, stub = NULL,
  genome = "hg19")

Arguments

x	a SummarizedExperiment-like object of some sort
toTDF	run igvtools totdf on the .GCT files? (default: no)
assay	the name of the assay to dump (default: assays(x)[[1]])
group	a grouping factor to dump by (default: dump everyone)
stub	the filename stub to dump (default: name of x, or x_group)
genome	the genome to use (default is hg19, due to annotations)

Value

list a list of filenames dumped

RamsinghLab/ozymandias documentation built on May 9, 2019, 9:21 a.m.