run.from.deseq.R

library(tfTarget)

#system variables


Half.size = 150
Min.size = 2500
Exp.cutoff = 2
Sites.num.cutoff = 10

#default variables

BigWig.path = "./"
Ncores = 1
MTH = 7
Run.repeats = 2
Pval.cutoff.up = 0.01
Pval.cutoff.down = 0.1
Fdr.cutoff = 0.05
Closest.N = NULL
Distance.cutoff = 1E6
deseq.only = F
rtfbsdb.only = F
Tfs.path =system.file("extdata", "tfs.rdata", package="tfTarget")

args<-commandArgs(TRUE)

tag.pos <- which(sapply(args,FUN=function(x) substr(x,1,1)=="-" ))
tag.pos <- c(tag.pos,length(args)+1)

#assign required arguments

Files.query = args[(which(args=="-query")+1):(tag.pos[which(tag.pos==which(args=="-query"))+1]-1)]
Files.control = args[(which(args=="-control")+1):(tag.pos[which(tag.pos==which(args=="-control"))+1]-1)]
Plus.files.query = Files.query[seq(1,length(Files.query),by=2)]
Minus.files.query = Files.query[seq(2,length(Files.query),by=2)]
Plus.files.control = Files.control[seq(1,length(Files.control),by=2)]
Minus.files.control = Files.control[seq(2,length(Files.control),by=2)]
Prefix = args[which(args == "-prefix")+1]
TRE.path = args[which(args=="-TRE.path")+1]
Gene.path = args[which(args=="-gene.path")+1]
File.twoBit = args[which(args=="-2bit.path")+1]


#assign optional arguments

if ("-bigWig.path" %in% args ) BigWig.path = args[which(args=="-bigWig.path")+1]
if ("-ncores" %in% args ) Ncores = as.numeric(args[which(args=="-ncores")+1])
if ("-mTH" %in% args ) MTH = as.numeric(args[which(args=="-mTH")+1])
if ("-cycles" %in% args ) Run.repeats = as.numeric(args[which(args=="-cycles")+1])
if ("-pval.up" %in% args ) Pval.cutoff.up = as.numeric(args[which(args=="-pval.up")+1])
if ("-pval.down" %in% args ) Pval.cutoff.down = as.numeric(args[which(args=="-pval.down")+1])
if ("-fdr.cutoff" %in% args ) Fdr.cutoff = as.numeric(args[which(args=="-fdr.cutoff")+1])
if ("-closest.N" %in% args ) Closest.N = as.numeric(args[which(args=="-closest.N")+1])
if ("-dist" %in% args ) Distance.cutoff = as.numeric(args[which(args=="-dist")+1])
if ("-tfs.path" %in% args ) Tfs.path = args[which(args=="-tfs.path")+1]



load(Tfs.path)



print("input file info")
cat("-bigWig.path:", BigWig.path, "\n")
cat("-query, plus files=", Plus.files.query, "\n")
cat("-query, minus files=", Minus.files.query, "\n")
cat("-control, plus files=", Plus.files.control, "\n")
cat("-control, minus files=", Minus.files.control, "\n")
cat("-TRE.path=", TRE.path, "\n")
cat("-gene.path=", Gene.path, "\n")


cat("\n")
print("motif enrichment parameters");
cat("-tfs.path=", Tfs.path, "\n");
cat("-mTH=", MTH, "\n");
cat("-cycles=", Run.repeats, "\n");
cat("-fdr.cutoff=", Fdr.cutoff, "\n");

cat("\n")
print("TRE-gene parameters");

cat("-dist=", Distance.cutoff, "\n")

if(is.null(Closest.N)) {
	cat("-closet.N= off \n")
} else {
	cat("-closet.N=", Closest.N, "\n")
}

cat("\n")
cat("running using ", Ncores, " cores", "\n")


#get deseq tables
print("loading diffTXN tables")

tfTar <-list(deseq.table.TRE = read.table(TRE.path,header=T,sep="\t"),
        deseq.table.gene = read.table(Gene.path,header=T,sep="\t"),
        gene.path = Gene.path,
        bigWig.path = BigWig.path,
        plus.files.query = Plus.files.control,
        plus.files.control = Plus.files.control,
        minus.files.query = Minus.files.query,
        minus.files.control = Minus.files.control,
        ncores= ncores)
class(tfTar)<-"tfTarget";


#run motif enrichment tests
print("running rtfbsdb")
tfTar <- searchTFBS(tfTar, tfs, File.twoBit, Pval.cutoff.up, Pval.cutoff.down, Half.size, MTH, Min.size, Run.repeats, ncores=Ncores)

#filter and cluster motifs (link motif to TRE)
print( "filtering motifs" )
tfTar <- filter.rtfbsdb(tfTar, Fdr.cutoff, Sites.num.cutoff, Exp.cutoff, ncores=Ncores)

print("plotting motifs")
#plot motif clustering and enrichment
plot( tfTar, Prefix)

#link TF, TRE and Gene
print("associating TFs to TREs and genes")
tfTar <- mapTF( tfTar, Prefix, Distance.cutoff, Closest.N);