default_download_filter_chip: Default filtering function for 'download_encode_chip'.

In ArnaudDroitLab/ef.utils: Eric Utilities

Description

The filtering function does three things:

1. It removes all files which do not have the correct genome assembly.

2. It removes broad marks chips, such as histones and Pol II.

3. If the provided results have been re-analyzed by the ENCODE Consortium, the ENCODE results are kept and the original ones discarded.

Usage

default_download_filter_chip(query.results, genome.assembly)

Arguments

query.results	A partial data.frame obtained from the queryEncode function.The biosample identifier from ENCODE. Valid examples are GM12878, K562.
genome.assembly	Which genome assembly should the results come from?

Value

A filtered data frame.

ArnaudDroitLab/ef.utils documentation built on Aug. 13, 2019, 9:09 p.m.