findFeatureOverlap {SVM2CRM} | R Documentation |
Find the overlap of genomic regions between the output of cisREfind and a database of validated cis-regulatory elements.
findFeatureOverlap(query, subject, select)
query |
database of validatated cis-regulatory elements (e.g. p300 binding sites), GRanges class. |
subject |
output cisREfindbed function, GRanges class. |
select |
parameters of findOverlaps |
See documentation of GenomicRanges for details.
A data frame with the genomic regions that overlap
Guidantonio Malagoli Tagliazucchi guidantonio.malagolitagliazucchi@unimore.it
cisREfind, findOverlaps, GenomicRanges
library("SVM2CRMdata") library("GenomicRanges") setwd(system.file("data",package="SVM2CRMdata")) load("CD4_matrixInputSVMbin100window1000.rda") completeTABLE<-CD4_matrixInputSVMbin100window1000 new.strings<-gsub(x=colnames(completeTABLE[,c(6:ncol(completeTABLE))]),pattern="CD4.",replacement="") new.strings<-gsub(new.strings,pattern=".norm.w100.bed",replacement="") colnames(completeTABLE)[c(6:ncol(completeTABLE))]<-new.strings setwd(system.file("extdata",package="SVM2CRMdata")) data_level2 <- read.table(file = "GSM393946.distal.p300fromTSS.txt",sep = "\t", stringsAsFactors = FALSE) data_level2<-data_level2[data_level2[,1]=="chr1",] DB <- data_level2[, c(1:3)] colnames(DB)<-c("chromosome","start","end") label <- "p300" table.final.overlap<-findFeatureOverlap(query=completeTABLE,subject=DB)