download_encode_chip: Obtains and process transcription factor data from ENCODE.

Description Usage Arguments Value

View source: R/EncodeHelper.R

Description

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

Usage

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

Arguments

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?

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 May 3, 2018, 11:23 p.m.