Mercurial > repos > davidecangelosi > pipe_t

comparison pipe-t.R @ 5:29a8df9f543d draft

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planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit a52ad1b746d5e5042b2114f5a9228d157b0e4787
author davidecangelosi
date Mon, 06 May 2019 06:33:33 -0400
parents e248cd7769e8
children d1cabb2bc795
comparison
equal deleted inserted replaced
4:e248cd7769e8 5:29a8df9f543d
391 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata) 391 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata)
392 rownames(phenoData)=as.vector(files$sampleName) 392 rownames(phenoData)=as.vector(files$sampleName)
393 raw<- readCtDataDav(files = as.vector(files$sampleName), header=FALSE, format="plain", path = path, sample.info=phenoData,n.features = as.numeric(nfeatures)) 393 raw<- readCtDataDav(files = as.vector(files$sampleName), header=FALSE, format="plain", path = path, sample.info=phenoData,n.features = as.numeric(nfeatures))
394 }, 394 },
395 "SDS"={ 395 "SDS"={
396 columns<- list(feature=3, Ct=6, flag=11) 396 #columns<- list(feature=3, Ct=6, flag=11)
397 columns <-SDS = list(flag = "Omit",feature = "Detector", type = "Task", position = "Wells", Ct = "Ct")
397 metadata <- data.frame(labelDescription = c("sampleName", "Treatment"), row.names = c("sampleName", "Treatment")) 398 metadata <- data.frame(labelDescription = c("sampleName", "Treatment"), row.names = c("sampleName", "Treatment"))
398 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata) 399 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata)
399 rownames(phenoData)=as.vector(files$sampleName) 400 rownames(phenoData)=as.vector(files$sampleName)
400 raw<- readCtDataDav(files = files$sampleName, format="SDS",column.info=columns, path = path, sample.info=phenoData, n.features=as.numeric(nfeatures)) 401 raw<- readCtDataDav(files = files$sampleName, format="SDS",column.info=columns, path = path, sample.info=phenoData, n.features=as.numeric(nfeatures))
401 }, 402 },