makeExpressionSet_ribo <- function(rnaCountFiles) {
# rnaExonCountFiles = list.files(file.path(dir,"data/rna"),pattern="*.txt",full.name=TRUE)
options(stringsAsFactors=FALSE)
require(parallel)
# RIBO file(s)
riboCountTable = read.table(riboCountFiles,sep="\t",header=T)
colnames(riboCountTable) = toupper(colnames(riboCountTable))
colnames(riboCountTable) = gsub(colnames(riboCountTable),
pattern=".",replace="",fixed=TRUE)
fData_ribo = riboCountTable[,-2]
fData_ribo = fData_ribo[order(fData_ribo$ENSGID),]
# GENE LENGTH
geneLen = data.frame(ENSGID=riboCountTable$ENSGID,len=riboCountTable$GENELENGTH)
# make expression data sets
require(Biobase)
featureData = new("AnnotatedDataFrame",data=data.frame(ENSGID=geneLen$ENSGID,len=geneLen$len))
rownames(fData_ribo) = fData_ribo[,1]
fData = fData_ribo[,-1]
pData = data.frame(seqData=rep("ribo",(NCOL(fData_ribo)-1)),
species=c(rep(c( rep("chimp",5),rep("human",6) ,
rep("rhesus",5)),1)),
celline=c(do.call(rbind,lapply(colnames(fData),
function(x) {xx=gsub(x,pattern=".rna",replace="");
xx=gsub(xx,pattern=".ribo",replace="");xx}))) )
rownames(pData) = colnames(fData)
metaData = data.frame(labelDescription=c("ribo data",
"human/chipmp/rhesus",
"name of cell line"),
row.names=c("seqData","species","celline"))
pData = new("AnnotatedDataFrame",data=pData,varMetadata=metaData)
experimentData <- new("MIAME",title="Ribo-seq cross species comparison")
eSet = ExpressionSet(assayData = as.matrix(fData),
phenoData=pData,
experimentData=experimentData)
featureData(eSet) = featureData
list(eSet=eSet,geneLen=geneLen)
}
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