createIndexes-methods {R3CPET} | R Documentation |
After loading the interactions and the TFBS, the createIndexes
method can be used to build indexes for fast
look-up for which which TF are located in which region. This method is an intermediate step needed for further analysis.
## S4 method for signature 'ChiapetExperimentData' createIndexes(object, minOverlap = 50)
object |
a |
minOverlap |
The minimum overlap between a TF binding site and a region, to consider a TF as binding to that region.
The default value is |
A ChiapetExperimentData
object in which the .dt
slot is populated as a data.table
object.
Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)
Mohamed Nadhir D, Yang C et al 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process, ....
ChiapetExperimentData
, loadTFBS
, loadPETs
, loadPPI
## get the different datasets path petFile <- file.path(system.file("example",package="R3CPET"),"HepG2_interactions.txt") tfbsFile <- file.path(system.file("example",package="R3CPET"),"HepG2_TF.txt.gz") ## Not run: x <- ChiapetExperimentData(pet = petFile, tfbs= tfbsFile, IsBed = FALSE, ppiType="HPRD", filter= TRUE) ## build the diffrent indexes x <- createIndexes(x) x ## End(Not run)