R3CPET (version 1.4.2)

CreateCenteredBED-methods: Create centered interactions

Description

This helper method can be used to create a "bed" file in which the coordinates of the regions are the centre of the interactions in the raw data. in R3CPET we suppose that the centre of the interactions are the most enriched when doing read mapping ,thus, we consider just the region around the centre to detect the TFBS.

Usage

"CreateCenteredBED"(file, header=TRUE,dist=1000)

Arguments

file

a character indicating the location of the rawdata file. the file should be a six column "bed" file in which the fist 3 columns indicate the left side interaction (chr, start, stop) and the other 3 columns indicate the right side interaction.

header

logical, indicates if the first line in the file is a header.

dist

numeric, indicated the distance around the center of the region to take.

Value

A 4 columns data.frame object, in which the first 3 columns indicate the location of the region and the 4th on indicate its name. The names are of the format PET#\w+.1 for the left side regions and PET#\w+.2 for the right side ones.

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")

res <- CreateCenteredBED(petFile, header=TRUE, dist=1000)
head(res)