ChIPInputMatch: Match the ChIP files with input files.

In chandlerzuo/mbasic: Matrix Based Analysis for State-space Inference and Clustering.

Description

Match the ChIP files with input files.

Usage

ChIPInputMatch(dir, suffices, depth = 5, celltypes)

Arguments

dir	A string vector of length 2. The first entry is the ChIP file directory and the second is the input file directory. It is required that ChIP and input files must be in two different directories.
suffices	A vector of strings for the suffices of each file name.
depth	The maximum depth under the dir paths that the files are stored. Default: 5.

Details

This function matches the ChIP files with the control files according to their filenames. The file names must follow the ENCODE consortium convention, i.e. the prefix of the file name is wgEncode<lab><experiment_type><cellline><factor><control>Aln[replicate]. Each string in <.> must has one single initial capital letter followed by lower case letters or digits.

Value

A data.frame object with the following fields:

chipfile	The name of the ChIP file.
inputfile	The prefix of the matching input files (i.e. without replicate identifiers).
lab	The string for the lab information.
experiment	The string for the experiment type.
cellline	The string for the cellline.
factor	The string for the factor.
control	The string for the control experiment.
chiptype	The file format of the ChIP data.
inputtype	The file format of the input data.

Author(s)

Chandler Zuo [e-mail]

Examples

## Not run:  ChIPInputMatch(c("ChIPDataDir/", "inputDataDir/"), suffices = ".tagAlign", depth = 2) 

chandlerzuo/mbasic documentation built on May 13, 2019, 3:24 p.m.