getSignal {SVM2CRM} | R Documentation |
This function simply model the signal of each histone marks around the features used in the input files and considering the bin.size and window size defined during the pre-processing step.
getSignal(bedfilelist,chr,reference,win.size,bin.size,label1="enhancers")
bedfilelist |
test_set produced for svm model |
chr |
a vector containin the list of chromsome that you want use during the analysis (e.g."chr1") |
reference |
file with the reference position of the features. The genomic coordinates of positive and negative examples (e.g. enhancers, not_enhancers) |
win.size |
windows size used to smooth the signal |
bin.size |
original bin size used |
label1 |
class of reference (e.g. enhancers or not_enhancers) |
Some detailled description
A data.frame with the signals where in the column there are the signals of the histone marks and in the rows the cis-regulatory elements.
Guidantonio Malagoli Tagliazucchi guidantonio.malagolitagliazucchi@unimore.it
cisREfindbed
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 #list_file<-grep(dir(),pattern=".sort.txt",value=TRUE) #train_positive<-getSignal(list_file,chr="chr1",reference="p300.distal.fromTSS.txt",win.size=500,bin.size=100,label1="enhancers") #train_negative<-getSignal(list_file,chr="chr1",reference="random.region.hg18.nop300.txt",win.size=500,bin.size=100,label1="not_enhancers") setwd(system.file("data",package="SVM2CRMdata")) load("train_positive.rda") load("train_negative.rda") training_set<-rbind(train_positive,train_negative) colnames(training_set)[c(5:ncol(training_set))]<-gsub(x=gsub(x=colnames(training_set[,c(5:ncol(training_set))]),pattern="sort.txt.",replacement=""),pattern="CD4.",replacement="")