loadTFBS-methods {R3CPET} | R Documentation |
This methods reads a BED file that contains the peak positions of different TF. All the TF peaks should be merged into one BED file that contains 4 columns that respectively contain the chromosome name, peak start, peak end, TF name.
## S4 method for signature 'ChiapetExperimentData,character' loadTFBS(object, tfbsFile,header=FALSE, ...)
object |
(Required) a |
tfbsFile |
(Required): path the BED file containing the position of the different TF binding site All the TF binding sites should be merged in this file as showed in this example: chr1 569820 569998 BHLHE40 chr1 936071 936346 BHLHE40 chr1 1014795 1015082 BHLHE40 ........................... ........................... chrY 13485240 13485769 ZBTB33 chrY 13488718 13489030 ZBTB33 chrY 15016340 15016848 ZBTB33 chrY 58843918 58844104 ZBTB33 |
header |
(optional) indicates if the provided BED file has a header or node. by default |
,
... |
reserved for later use. |
A ChiapetExperimentData
object in which the tfbs
slot is populated as a GRanges
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
, loadPPI
, createIndexes
## Create a ChiapetExperimentData object x <- ChiapetExperimentData(ppiType= "HPRD") ## load TFBS tfbsFile <- file.path(system.file("example",package="R3CPET"),"HepG2_TF.txt.gz") x <- loadTFBS(x,tfbsFile=tfbsFile) tfbs(x)