loadTFBS-methods: Loading TF binding sites

In R3CPET: 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

Description

This methods reads a BED file that contains the peak positions of different TF. All the TF peaks should be merged into one BED file that contains 4 columns that respectively contain the chromosome name, peak start, peak end, TF name.

Usage

## S4 method for signature 'ChiapetExperimentData,character'
loadTFBS(object, tfbsFile,header=FALSE, ...)

Arguments

object	(Required) a ChiapetExperimentData object
tfbsFile	(Required): path the BED file containing the position of the different TF binding site All the TF binding sites should be merged in this file as showed in this example: chr1 569820 569998 BHLHE40 chr1 936071 936346 BHLHE40 chr1 1014795 1015082 BHLHE40 ........................... ........................... chrY 13485240 13485769 ZBTB33 chrY 13488718 13489030 ZBTB33 chrY 15016340 15016848 ZBTB33 chrY 58843918 58844104 ZBTB33
header	(optional) indicates if the provided BED file has a header or node. by default header=FALSE

,

...	reserved for later use.

Value

A ChiapetExperimentData object in which the tfbs slot is populated as a GRanges object.

Author(s)

Mohamed Nadhir Djekidel ([e-mail])

References

Mohamed Nadhir D, Yang C et al 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process, ....

See Also

ChiapetExperimentData, loadTFBS , loadPPI, createIndexes

Examples

## Create a ChiapetExperimentData object
x <- ChiapetExperimentData(ppiType= "HPRD")

## load TFBS
tfbsFile <- file.path(system.file("example",package="R3CPET"),"HepG2_TF.txt.gz")
x <- loadTFBS(x,tfbsFile=tfbsFile)
tfbs(x)

R3CPET documentation built on Nov. 8, 2020, 8:05 p.m.