PrepareData-methods {R3CPET} | R Documentation

## Loading the raw data all at once

### Description

Instead of loading the data one at a time and then creating the index using the methods `loadPETs`,`loadTFBS` and `createIndexes`. The user can directly use the method `PrepareData` to do that.

### Usage

    ## S4 method for signature 'character,character,logical'
    PrepareData(petFile,tfbsFile, petIsBed=TRUE)

### Arguments

`petFile` | a `character` specifying the path to the interaction file. it the file is in a "bed" format `petIsBed` should be `TRUE`. The data should be formated as described in `loadPETs`.
`tfbsFile` | a `character` specifying the path to the transcription factors binding site file. The data should be formated as described in `loadTFBS`.
`petIsBed` | a logical value specifying if the interaction file is in a "bed" format or not.

### Value

A `ChiapetExperimentData` object in which the `pet`,`tfbs` and `.dt` slots populated .

### 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` , `loadPETs`, `loadPPI`, `createIndexes`.

### Examples

        ## get interactions file location
        petFile <- file.path(system.file("example",package="R3CPET"),"HepG2_interactions.txt")

        ## get the TFBS file location
        tfFile <- file.path(system.file("example",package="R3CPET"),"HepG2_TF.txt.gz")

        ## Not run:
        ## load the data
        x<- PrepareData(petFile, tfFile, FALSE)
        x

    ## End(Not run)

[Package R3CPET version 1.22.0 Index]