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medips 2014-02
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source("http://bioconductor.org/biocLite.R") | |
#biocLite("BSgenome") | |
## GTOOLS AND GDATA INSTALLED FROM SOURCES `R CMD INSTALL archive.tar.gz` | |
#biocLite("edgeR") | |
#biocLite("DNAcopy") | |
#biocLite("Rsamtools") | |
#biocLite("rtracklayer") | |
#biocLite("MEDIPS") | |
#biocLite("BSgenome.Rnorvegicus.UCSC.rn5") | |
library(MEDIPS) | |
library(BSgenome.Rnorvegicus.UCSC.rn5) | |
#genome <- | |
genome <- "BSgenome.Rnorvegicus.UCSC.rn5" | |
#MEDIPS will replace all reads which map to exactly the same start and end | |
#positions on the same strand by only one representative: | |
uniq=TRUE | |
#All reads will be extended to a length of 300nt according to the given strand | |
#information | |
extend=300 | |
shift=0 | |
#The genome will be divided into adjacent windows of length 100nt and | |
ws=50 | |
print(seqnames(BSgenome.Rnorvegicus.UCSC.rn5::Rnorvegicus)) | |
myCreateSet <- function(name,genome,chromosome) | |
{ | |
return ( MEDIPS.createSet( | |
file = paste("/commun/data/projects/20130607.AC1WR3ACXX.MEDIPSEQ/align/Samples/",name,"/BAM/",name,"_final.bam",sep=""), | |
BSgenome = genome, | |
extend = extend, | |
shift = shift, | |
uniq = uniq, | |
window_size = ws, | |
chr.select = chromosome | |
)) | |
} | |
myCreateSet2 <- function(names,genome,chromosome) | |
{ | |
dataset <- NULL | |
for(N in names) | |
{ | |
if(is.null(dataset)) | |
{ | |
dataset <- myCreateSet(N,genome,chr.select) | |
} | |
else | |
{ | |
dataset <- c( dataset , myCreateSet(N,genome,chr.select)) | |
} | |
} | |
return (dataset) | |
} | |
myMedipAnalysis<- function(dataSet1, dataSet2, name,genome,chromosome) | |
{ | |
filename2 <- paste("medip.",name,".merge.",chromosome,".tsv",sep="") | |
if( chromosome=="chrX") | |
{ | |
return (0); | |
} | |
if( chromosome == "chr14" && ( name=="20L_vs_8H" || name=="20L_vs_8L" || name=="20H_vs_8L" || name=="20H_vs_8H" || name=="8H_vs_8L") ) | |
{ | |
return (0); | |
} | |
write(paste(">>>>> NOW2: ",filename2), stderr()) | |
if(file.exists(filename2)) return (0); | |
CS <- MEDIPS.couplingVector(pattern = "CG", refObj = dataSet1[[1]]) | |
write(paste(">>>>> NOW12 ",filename2), stderr()) | |
is.medip <- TRUE | |
if( chromosome == "chr14" && (name=="20H_vs_20L" || name=="20H_vs_8H" || name=="20H_vs_8L" || name=="20L_vs_8H")) | |
{ | |
is.medip <- FALSE | |
} | |
mr.edgeR = MEDIPS.meth( | |
MSet1 = dataSet1, | |
MSet2 = dataSet2, | |
CSet = CS, | |
p.adj = "bonferroni", | |
diff.method = "edgeR", | |
prob.method = "poisson", | |
MeDIP = is.medip , | |
CNV = F, type = "rpkm", | |
minRowSum = 1 | |
) | |
write(paste(">>>>> NOW3: ",filename2), stderr()) | |
mr.edgeR.s = MEDIPS.selectSig(results = mr.edgeR, p.value = 0.1,adj = T, ratio = NULL, bg.counts = NULL, CNV = F) | |
summary( mr.edgeR.s ) | |
write(paste(">>>>> NOW4: ",filename2), stderr()) | |
mr.edgeR.s.gain = mr.edgeR.s[which(mr.edgeR.s[, grep("logFC", colnames(mr.edgeR.s))] > 0), ] | |
write(paste(">>>>> NOW5: ",filename2), stderr()) | |
summary( mr.edgeR.s.gain ) | |
write.table( mr.edgeR.s.gain , file=paste("medip.",name,".gain.",chromosome,".tsv",sep="") ,sep="\t",col.names=TRUE) | |
summary(mr.edgeR.s.gain) | |
if( nrow( mr.edgeR.s.gain) ==0 ) return (0) | |
write(paste(">>>>> NOW6: ",filename2), stderr()) | |
mr.edgeR.s.gain.m = MEDIPS.mergeFrames(frames = mr.edgeR.s.gain, distance = 1) | |
write.table( mr.edgeR.s.gain.m , file=filename2 ,sep="\t",col.names=TRUE) | |
return (0) | |
} | |
chromosomes <- seqnames(BSgenome.Rnorvegicus.UCSC.rn5::Rnorvegicus); | |
for(chr.select in chromosomes) | |
{ | |
Set20H <- myCreateSet2(c("20H1-1","20H1-3","20H1-4","20H2-1","20H5-1","20H5-2"),genome,chr.select) | |
Set20L <- myCreateSet2(c("20L1-1","20L1-2","20L3-1","20L3-2","20L6-2","20L7-1"),genome,chr.select) | |
Set8H <- myCreateSet2(c("8H1-1","8H1-4","8H2-2","8H3-1","8H3-2","8H5-2"),genome,chr.select) | |
Set8L <- myCreateSet2(c("8L1-2","8L3-4","8L6-1","8L6-2","8L8-1","8L8-4"),genome,chr.select) | |
myMedipAnalysis(Set20H,Set20L,"20H_vs_20L",genome,chr.select) | |
myMedipAnalysis(Set20H,Set8H,"20H_vs_8H",genome,chr.select) | |
myMedipAnalysis(Set20H,Set8L,"20H_vs_8L",genome,chr.select) | |
myMedipAnalysis(Set20L,Set8H,"20L_vs_8H",genome,chr.select) | |
myMedipAnalysis(Set20L,Set8L,"20L_vs_8L",genome,chr.select) | |
myMedipAnalysis(Set8H,Set8L,"8H_vs_8L",genome,chr.select) | |
} |
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