--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/AskoR_DE.R	Thu Apr 12 05:23:45 2018 -0400
@@ -0,0 +1,44 @@
+askor_path<-Sys.getenv("ASKOR_PATH")
+source(paste0(askor_path,"/AskoR.R"))
+
+##############################################
+##                Parameters                ##
+##############################################
+
+parameters<-Asko_start()
+setwd(parameters$dir_path)
+# source("/home/flegeai/local/askoR/askoStart.R")
+#parameters$col_genes=1
+#parameters$col_counts=7
+# parameters$regex=FALSE
+#parameters$rm_sample=list("T0_4", "T1K_4", "T1A_4", "T2A_4", "T2K_4", "T3K_4", "T3A_4")
+# #parameters$select_sample=c("T0_4", "T1K_4", "T1A_4", "T2A_4", "T2K_4", "T3K_4", "T3A_4")
+# #parameters$rm_sample=list("_4")
+# parameters$organism = "Ap"
+# parameters$fileofcount = NULL
+# parameters$annotation_file = "annotation.txt"
+# parameters$sample_file = "Samples.txt"
+# parameters$contrast_file = "Contrasts.txt"
+# parameters$mk_context="manual"
+# parameters$glm="qlf"
+
+
+########################################
+##  Loading the data from the samples ##+
+########################################
+
+data<-loadData(parameters)
+cat("Total number of genes : ", dim(data$dge$counts)[1], "\n")
+cat("Total number of samples : ", dim(data$dge$counts)[2], "\n")
+cat("summary of CPM by samples\n")
+summary(cpm(data$dge))
+pdf(parameters$output_pdf)
+asko_data<-asko3c(data)
+cat("Filtering genes with more than ", parameters$threshold_cpm, " CPM in ",parameters$replicate_cpm,"samples\n")
+asko_filt<-GEfilt(data$dge, parameters)
+cat("Total number of filtered genes : ", dim(asko_filt$counts)[1], "\n")
+asko_norm<-GEnorm(asko_filt,parameters)
+GEcorr(asko_norm,parameters)
+cat("Statistical analysis\n")
+DEanalysis(asko_norm,data, asko_data,parameters)
+dev.off()