download_encode_chip: Obtains and process transcription factor data from ENCODE.
In ArnaudDroitLab/ef.utils: Eric Utilities

Given an encode biosample identifier (GM12878, MCF-7, etc.), this function retrieved processed bed files giving the genomic location of binding peaks.

download_encode_chip(biosample, assembly,
  download.filter = default_download_filter_chip,
  download.dir = file.path("input/ENCODE", biosample, assembly, "chip-seq"),
  keep.signal = FALSE)

`biosample`	The biosample identifier from ENCODE. Valid examples are GM12878, K562 or MCF-7.
`download.filter`	A filtering function to be applied to the experiment data-frame returned by `queryEncode`. The function should return a filtered `data-frame` containing only the files which should be downloaded.
`download.dir`	The folder where the downloaded files should be stored. defaults to `file.path("input/ENCODE", biosample, "chip-seq")`.
`keep.signal`	Should the signalValue from the ChIP-seq be kept?
`genome.assembly`	Which genome assembly should the results come from?

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.