Mercurial > repos > genouest > askor_de

comparison AskoR_DE.R @ 2:877d2be25a6a draft default tip

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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/askor commit 994ecff7807bb0eb9dac740d67ad822415b0b464
author genouest
date Thu, 19 Apr 2018 03:44:31 -0400
parents ceef9bc6bbc7
children
comparison
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1:6bbc90a11c3f 2:877d2be25a6a
1 askor_path<-Sys.getenv("ASKOR_PATH") 1 askor_path<-Sys.getenv("ASKOR_PATH")
2 source(paste0(askor_path,"/AskoR.R")) 2 source(paste0(askor_path,"/AskoR.R"))
3 3
4 ############################################## 4 ##############################################
5 ## Parameters ## 5 ## Parameters ##
6 ############################################## 6 ##############################################
7 7
8 parameters<-Asko_start() 8 parameters<-Asko_start()
9 setwd(parameters$dir_path) 9 setwd(parameters$dir_path)
10 # source("/home/flegeai/local/askoR/askoStart.R") 10 # source("/home/flegeai/local/askoR/askoStart.R")
29 29
30 data<-loadData(parameters) 30 data<-loadData(parameters)
31 cat("Total number of genes : ", dim(data$dge$counts)[1], "\n") 31 cat("Total number of genes : ", dim(data$dge$counts)[1], "\n")
32 cat("Total number of samples : ", dim(data$dge$counts)[2], "\n") 32 cat("Total number of samples : ", dim(data$dge$counts)[2], "\n")
33 cat("summary of CPM by samples\n") 33 cat("summary of CPM by samples\n")
34 summary(cpm(data$dge)) 34 summary(cpm(data$dge, normalized.lib.sizes=FALSE))
35 pdf(parameters$output_pdf) 35 pdf(parameters$output_pdf)
36 asko_data<-asko3c(data) 36 asko_data<-asko3c(data)
37 cat("Filtering genes with more than ", parameters$threshold_cpm, " CPM in ",parameters$replicate_cpm,"samples\n") 37 cat("Filtering genes with more than ", parameters$threshold_cpm, " CPM in ",parameters$replicate_cpm,"samples\n")
38 asko_filt<-GEfilt(data$dge, parameters) 38 asko_filt<-GEfilt(data$dge, parameters)
39 cat("Total number of filtered genes : ", dim(asko_filt$counts)[1], "\n") 39 cat("Total number of filtered genes : ", dim(asko_filt$counts)[1], "\n")
40 asko_norm<-GEnorm(asko_filt,parameters) 40 asko_norm<-GEnorm(asko_filt,parameters)
41 GEcorr(asko_norm,parameters) 41 GEcorr(asko_norm,parameters)
42 cat("Statistical analysis\n") 42 cat("Statistical analysis\n")
43 DEanalysis(asko_norm,data, asko_data,parameters) 43 DEanalysis(asko_norm,data, asko_data,parameters)
44 dev.off() 44 dev.off()
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