findFeatureOverlap: Find the overlap of genomic regions between the output of...

Description Usage Arguments Details Value Author(s) See Also Examples

Description

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

Usage

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    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

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    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)


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