R: Loading the raw data all at once

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, ....

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 1.20.0 Index]