R3CPET (version 1.4.2)

loadPETs-methods: Parsing ChIA-PET interaction data

Description

This method loads the ChIA-PET interactions data into a GRanges object from a file generated by ChIA-PET tool or an already formatted BED file.

Usage

"loadPETs"(object, petFile, IsBed=TRUE, header=TRUE, dist=1000)

Arguments

object

(Required) a ChiapetExperimentData object

petFile

(Required) path to the file to parse. two types of formats are accepted. If the file comes from the ChIA-PET tool or has the same format used in the ENCODE project

  chromleft startleft endleft chromright startright endright
      chr1    872113  879175       chr1     933836   938416     
      chr1    874165  879175       chr1     933340   938306     
      chr1    889676  896594       chr1     933897   938982     
      chr1    898753  907581       chr1     931133   939571     
      chr1    910103  918775       chr1     930834   938627     
      chr1    919314  922154       chr1     934212   937864      

only the the coordinates of the left and the right regions are considered (which means the first 6 columns), The additional columns are just ignored. We suppose that the user has already selected the interactions that sound significant for him.

if this kind of file is provided the IsBed parameter should be set to FASLE. if the file has no header the user needs to set header=FALSE.

if IsBed parameter is provided, the provided file should have 4 columns, three to describe the region location and the forth column to indicate the ID of the interaction and its position (1: for left and 2: for right), according to following pattern PET#\d\.1 or PET#\d\.2.

      	chr1	  1241234	  1242234	PET#1.1
      	chr1	  1242724	  1243724	PET#1.2
      	chr1	  1282708	  1283708	PET#2.1
      	chr1	  1283834	  1284834	PET#2.2
      	chr1	  1370871	  1371871	PET#3.1
      	chr1	  1372322	  1373322	PET#3.2

IsBed

(optional) The flag indicates whether the provided file has a 4 columns BED (when IsBed = TRUE ) format or has the ChIA-PET tool format (when IsBed = FALSE). By default, IsBed = TRUE

header

(optional) Indicates whether or not the first line of the file should be considered as a header. by default it is TRUE

dist

(optional) This parameter indicates the size of the up- and down-stream regions (in bp) to consider around the center of each region. 3CPET is based on the assumption that the real ChIP-Seq signal is more enriched around the center of the regions and get more depleted when moving further in both directions. Thus, when the user provides a file that has a ChIA-PET tool format (IsBed = TRUE), 3CPET will first center the regions and consider only distance bp up- and down-stream of the center of each region. A default value of 1000bp is used.

Value

A ChiapetExperimentData object in which the ppi is populated as a GRanges object.

References

Li G, Fullwood MJ, Xu H et al.ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biology 2010, 11(2):R22

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 the different datasets (where the file has a Chia-PET tool format )
petFile <- file.path(system.file("example",package="R3CPET"),"HepG2_interactions.txt")
x <- loadPETs(x, petFile=petFile, IsBed=FALSE)

## when loading an already formatted BED file
petFile <- file.path(system.file("example",package="R3CPET"),"HepG2_centered.bed")
x <- loadPETs(x, petFile=petFile, IsBed=TRUE, header=FALSE)

pet(x)