generateSyntheticData: Generate synthetic BED data, M and GC files.

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

Description

This function generates three set of files. ChIP BED files are stored in 'chip/', input BED files are stored in 'input/', mappability and GC files are stored in 'mgc/'. All BED files follow the name convention for the ENCODE consortium. Each chromosome has a size of 10K, and each locus has 20 bp. ChIP data for two celllines, each with K transcription factors, are generated. All ChIP experiments with the same celltype have the same matching input. Each ChIP experiment has randomly 1-3 replicates. Each input has 3 replicates.

Usage

generateSyntheticData(dir, nchr = 5, K = 5, I = 100, J = 3)

Arguments

dir	The directory for the generated datasets. If this directory already exists, it will be removed before being recreated.
nchr	The number of chromosomes. Default: 5.
K	The number of different transcription factors. Default: 5.
I	The number of loci. Default: 100.
J	The number of clusters among the loci. Default: 3.

Value

A RangedData object.

Author(s)

Chandler Zuo [e-mail]

Examples

## Not run: generateSyntheticData("tmpData/", nchr = 5, K = 5, I = 100, J = 3) 

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