R3CPET (version 1.4.2)

PrepareData-methods: 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

"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 .

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)