R3CPET (version 1.4.2)

loadTFBS-methods: Loading TF binding sites

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

"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.

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)