download_encode_histones: Helper function for obtaining histone data through...

Description Usage Arguments Value

View source: R/EncodeHelper.R

Description

Helper function for obtaining histone data through download_encode_chip.

Usage

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download_encode_histones(biosample, assembly,
  download.dir = file.path("input/ENCODE", biosample, assembly, "chip-seq",
  "histones"), ...)

Arguments

biosample

The biosample identifier from ENCODE. Valid examples are GM12878, K562 or MCF-7.

download.dir

The folder where the downloaded files should be stored. defaults to file.path("input/ENCODE", biosample, assembly, "chip-seq", "tf").

...

Other parameters to be passed to download_encode_chip.

genome.assembly

Which genome assembly should the results come from?

Value

A list containing three elements:

Metadata

The metadata returned by queryEncode, containing information about all files which matched the query.

Downloaded

The list of files which were downloaded.

Regions

The processed peak regions.


ArnaudDroitLab/ef.utils documentation built on Nov. 24, 2018, 5:11 p.m.