better table export

dge_workflow/dge_analysis.R

 #!/usr/bin/env Rscript
-
 #+ setup, cache=FALSE
 
 suppressMessages(require(docopt))
@@ -14,9 +13,9 @@ Options:
 -S                     Dont do general statistics and qc analysis
 '
 
-
 #opts <- docopt(doc, commandArgs(TRUE)) ## does not work when spining
 #opts <- docopt(doc, "--undirected ..")
+# opts <- docopt(doc, paste(Sys.getenv("DGE_PARAMS"), ".."))
 
 opts <- docopt(doc, paste(Sys.getenv("DGE_PARAMS"), paste(commandArgs(TRUE), collapse=" ")))
 #opts
@@ -61,7 +60,10 @@ cuff <- readCufflinks(dir=tmpdir)
 
 cuff
 runInfo(cuff)
-replicates(cuff) %>% mutate(file=basename(file)) %>% select(-c(total_mass, norm_mass, internal_scale, external_scale))
+replicateInfo <- replicates(cuff) %>% mutate(file=basename(file)) %>% select(-c(total_mass, norm_mass, internal_scale, external_scale))
+write.delim(replicateInfo, file="replicateInfo.txt")
+# replicateInfo <- read.delim("replicateInfo.txt")
+#'  [replicateInfo](replicateInfo.txt)
 
 #+ eval=skipQC
 #hello hidden field
@@ -89,56 +91,44 @@ if(!file.exists(cacheFile)){
 #colnames(gFpkmMatrix) <- ifelse(is.na(sampleDic[colnames(gFpkmMatrix)]), colnames(gFpkmMatrix), sampleDic[colnames(gFpkmMatrix)])
 fpkmMatrix(genes(cuff)) %>%
     rownames2column("ensembl_gene_id") %>%
-    merge(geneInfo, by.x="ensembl_gene_id", all.x=T) %>%
-    write.delim(file="geneFpkmWithInfo.txt")
-# geneFpkmWithInfo <- read.delim("geneFpkmWithInfo.txt")
-#' [Annotated Expresssion Table](geneFpkmWithInfo.txt)
+    merge(geneInfo, by="ensembl_gene_id", all.x=T) %>%
+    print_head() %>%
+    write.delim(file="gene_fpkm.txt")
+# gene_fpkm <- read.delim("gene_fpkm.txt")
+#' [Annotated Expresssion Table](gene_fpkm.txt)
 
 ## export the same but now including replicate information
 
-
-
 repFpkmMatrix(genes(cuff)) %>%
     rownames2column("ensembl_gene_id") %>%
-    merge(geneInfo, by.x="ensembl_gene_id", all.x=T) %>%
-    write.delim(file="geneReplicateFpkmWithInfo.txt")
-# geneFpkmWithInfo <- read.delim("geneReplicateFpkmWithInfo.txt")
-#' [Annotated Expresssion Table](geneReplicateFpkmWithInfo.txt)
-
-#+ eval=FALSE, echo=FALSE
-## DEBUG start
-if(F){
-read.delim("geneReplicateFpkmWithInfo.txt") %>%
-filter(external_gene_name=="Insm1") %>%
-melt() %>%
-ggplot(aes(variable, value)) + geom_bar(stat="identity")
-}
-## DEBUG end
-
-
-geneFpkm<-fpkm(genes(cuff))
-
-#ggplot(geneFpkm, aes(fpkm)) + geom_histogram() + scale_x_log10()
-
-write.delim(geneFpkm, file="geneFpkm.txt")
-# gene.fpkm <- read.delim("gene.fpkm.txt")
-
-write.delim(repGeneFPKMs, file="repGeneFPKMs.txt")
-# repGeneFPKMs <- read.delim("repGeneFPKMs.txt")
-# repGeneFPKMs <- local(get(load("repGeneFPKMs.RData")))
-#'  [FPKMs by Replicate](repGeneFPKMs.txt)
-
-geneCounts<-count(genes(cuff))
-#max(geneCounts$count)
-write.delim(geneCounts, file="geneCounts.txt")
-geneCgene.matrix<-fpkmMatrix(genes(cuff))
-#'  [Raw Counts](geneCounts.txt)
+    merge(geneInfo, by="ensembl_gene_id", all.x=T) %>%
+    print_head() %>%
+    write.delim(file="gene_fpkm_by_replicate.txt")
+# gene_fpkm <- read.delim("gene_fpkm_by_replicate.txt")
+#' [Annotated Expresssion Table](gene_fpkm_by_replicate.txt)
+
+fpkm(genes(cuff)) %>%
+    dplyr::rename(ensembl_gene_id=gene_id) %>%
+    merge(geneInfo, by="ensembl_gene_id", all.x=T) %>%
+    write.delim(file="geneFpkm.txt")
+
+
+count(genes(cuff)) %>%
+    dplyr::rename(ensembl_gene_id=gene_id) %>%
+    merge(geneInfo, by="ensembl_gene_id", all.x=T)
+    write.delim(file="geneCounts.txt")
+# geneCounts <- read.delim("geneCounts.txt")
+#'  [Gene Fragment Counts](geneCounts.txt)
+
+countMatrix(genes(cuff)) %>%
+    dplyr::rename(ensembl_gene_id=gene_id) %>%
+    merge(geneInfo, by="ensembl_gene_id", all.x=T)
+    write.delim(file="replicateCounts.txt")
+# repCounts <- read.delim("replicateCounts.txt")
+#'  [Raw Counts by Replicate](replicateCounts.txt)
+
+##ggplot(geneFpkm, aes(fpkm)) + geom_histogram() + scale_x_log10()
 
-repCounts <- countMatrix(genes(cuff))
-write.delim(repCounts, file="repCounts.txt")
-# repCounts <- read.delim("repCounts.txt")
-#'  [Raw Counts by Replicate](repCounts.txt)
-## tt
 
 #######################################################################################################################
 #' ## Score Distributions