findFeatureOverlap {SVM2CRM}R Documentation

Find the overlap of genomic regions between the output of cisREfind and a database of validated cis-regulatory elements.

Description

Find the overlap of genomic regions between the output of cisREfind and a database of validated cis-regulatory elements.

Usage

    findFeatureOverlap(query, subject, select)

Arguments

query

database of validatated cis-regulatory elements (e.g. p300 binding sites), GRanges class.

subject

output cisREfindbed function, GRanges class.

select

parameters of findOverlaps

Details

See documentation of GenomicRanges for details.

Value

A data frame with the genomic regions that overlap

Author(s)

Guidantonio Malagoli Tagliazucchi guidantonio.malagolitagliazucchi@unimore.it

See Also

cisREfind, findOverlaps, GenomicRanges

Examples

    
    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)
[Package SVM2CRM version 1.12.0 Index]