loadPETs-methods: Parsing ChIA-PET interaction data

In sirusb/R3CPET: 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

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

## S4 method for signature 'ChiapetExperimentData,character'
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.

Author(s)

Mohamed Nadhir Djekidel ([e-mail])

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)

sirusb/R3CPET documentation built on Oct. 12, 2020, 6 p.m.