loadTFBS-methods {R3CPET} | R Documentation

## 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

    ## 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 (nde12@mails.tsinghua.edu.cn)

### 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)

[Package R3CPET version 1.12.0 Index]