motifHist: Motif histogram

In alexjgriffith/CCCA: Cross Condition ChIP Analyisis

Description

Motif histogram

Usage

motifHist(data, mList, cList, locationsM, locationsC, n1, n2, reg,
  one = FALSE)

Examples

values<-loadHeightFile(heightFile)
data<-values$data
reg<-ascore(data,1,"top",3)
test<-readDNAStringSet(fastaFile,use.names = TRUE)
motifs<-as.matrix(read.table("data/normal_not_abnormal_motifs"))
mList<-unlist(lapply(c(motifs,addmotifs),IUPACtoBase))
cList<-unlist(lapply(lapply(c(motifs,"CGNNGC"),IUPACtoBase),compliment))
locationsM<-lapply(mList,grep,test)
locationsC<-lapply(cList,grep,test)
l<-length(cList)
motifHist(mList,cList,locationsM,locationsC,4,l,reg)

alexjgriffith/CCCA documentation built on May 10, 2019, 8:52 a.m.