Mercurial > repos > davidecangelosi > pipe_t

comparison pipe-t.R @ 8:e5953805ad7a draft

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planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 7d54176ff26ed5f4411edb0582a3704dd90253c0
author davidecangelosi
date Tue, 07 May 2019 06:05:32 -0400
parents 3e099c082954
children 69f5c4d6e6bd
comparison
equal deleted inserted replaced
7:3e099c082954 8:e5953805ad7a
398 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata) 398 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata)
399 rownames(phenoData)=as.vector(files$sampleName) 399 rownames(phenoData)=as.vector(files$sampleName)
400 raw<- readCtDataDav(files = as.vector(files$sampleName), header=FALSE, format="plain", path = path, sample.info=phenoData,n.features = as.numeric(nfeatures)) 400 raw<- readCtDataDav(files = as.vector(files$sampleName), header=FALSE, format="plain", path = path, sample.info=phenoData,n.features = as.numeric(nfeatures))
401 }, 401 },
402 "SDS"={ 402 "SDS"={
403 #columns<- list(feature=3, Ct=6, flag=11) 403 columns<- list(feature=3, Ct=6, flag=11)
404 columns <-list(flag = "Omit",feature = "Detector", type = "Task", position = "Wells", Ct = "Avg.Ct") 404 #columns <-list(flag = "Omit",feature = "Detector", type = "Task", position = "Wells", Ct = "Avg.Ct")
405 metadata <- data.frame(labelDescription = c("sampleName", "Treatment"), row.names = c("sampleName", "Treatment")) 405 metadata <- data.frame(labelDescription = c("sampleName", "Treatment"), row.names = c("sampleName", "Treatment"))
406 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata) 406 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata)
407 rownames(phenoData)=as.vector(files$sampleName) 407 rownames(phenoData)=as.vector(files$sampleName)
408 raw<- readCtDataDav(files = files$sampleName, format="SDS",column.info=columns, path = path, sample.info=phenoData, n.features=as.numeric(nfeatures)) 408 raw<- readCtDataDav(files = files$sampleName, format="SDS",column.info=columns, path = path, sample.info=phenoData, n.features=as.numeric(nfeatures))
409 }, 409 },