@sjcrh/proteinpaint-server 2.29.1 → 2.29.3

package/utils/edge.R

@@ -0,0 +1,86 @@
+# json='{"case":"SJMB066856,SJMB069601,SJMB030827,SJMB030838,SJMB031131,SJMB031227,SJMB077221,SJMB077223","control":"SJMB069596,SJMB069587,SJMB074736,SJMB030488,SJMB030825,SJMB031110,SJMB032998,SJMB033002","input_file":"/Users/rpaul1/pp_data/files/hg38/sjmb12/rnaseq/geneCounts.txt"}' && time echo $json | Rscript edge.R
+
+# json='{"case":"SJMB030827,SJMB030838,SJMB064540,SJMB064538,SJMB064520,SJMB064535,SJMB031131,SJMB031227","control":"SJMB030488,SJMB030825,SJMB064537,SJMB064510,SJMB064533,SJMB064534,SJMB031110","input_file":"/Users/rpaul1/pp_data/files/hg38/sjmb12/rnaseq/geneCounts.txt"}' && time echo $json | Rscript edge.R
+
+# Checking if all R packages are installed or not, if not installing each one of them
+
+jsonlite_path <- system.file(package='jsonlite')
+if (nchar(jsonlite_path) == 0) {
+  install.packages("jsonlite", repos='https://cran.case.edu/')
+}
+
+edgeR_path <- system.file(package='edgeR')
+if (nchar(edgeR_path) == 0) {
+  BiocManager::install("edgeR")
+}
+
+readr_path <- system.file(package='readr')
+if (nchar(readr_path) == 0) {
+  install.packages("readr", repos='https://cran.case.edu/')
+}
+
+
+library(jsonlite)
+library(stringr)
+library(readr)
+suppressWarnings({
+    suppressPackageStartupMessages(library(edgeR))
+    suppressPackageStartupMessages(library(dplyr))
+})
+
+infile <- file("stdin")
+input <- fromJSON(infile)
+print (input$output_path)
+cases <- unlist(strsplit(input$case, ","))
+controls <- unlist(strsplit(input$control, ","))
+combined <- c("geneID","geneSymbol",cases,controls)
+#data %>% select(all_of(combined))
+read_file_time_start <- Sys.time()
+read_counts <- read_tsv(input$input_file, col_names = TRUE, col_select = combined)
+geneIDs <- unlist(read_counts[1])
+geneSymbols <- unlist(read_counts[2])
+read_counts <- select(read_counts, -geneID)
+read_counts <- select(read_counts, -geneSymbol)
+read_file_time_stop <- Sys.time()
+print (read_file_time_stop - read_file_time_start)
+
+diseased <- rep("Diseased", length(cases))
+control <- rep("Control", length(controls))
+conditions <- c(diseased, control)
+tabs <- rep("\t",length(geneIDs))
+gene_id_symbols <- paste0(geneIDs,tabs,geneSymbols)
+y <- DGEList(counts = as.matrix(read_counts), group = conditions, genes = gene_id_symbols)
+keep <- filterByExpr(y)
+y <- y[keep, keep.lib.sizes = FALSE]
+y <- calcNormFactors(y, method = "TMM")
+#print (y)
+calculate_DE_time_start <- Sys.time()
+dge <- estimateDisp(y = y)
+et <- exactTest(object = dge)
+calculate_DE_time_stop <- Sys.time()
+print ("Time to calculate DE")
+print (calculate_DE_time_stop - calculate_DE_time_start)
+#print (et)
+logfc <- et$table$logFC
+logcpm <- et$table$logCPM
+pvalues <- et$table$PValue
+genes_matrix <- str_split_fixed(unlist(et$genes),"\t",2)
+geneids <- unlist(genes_matrix[,1])
+genesymbols <- unlist(genes_matrix[,2])
+adjust_p_values <- p.adjust(pvalues, method = "fdr")
+
+output <- data.frame(geneids,genesymbols,logfc,-log10(pvalues),-log10(adjust_p_values))
+names(output)[1] <- "gene_name"
+names(output)[2] <- "gene_symbol"
+names(output)[3] <- "fold_change"
+names(output)[4] <- "original_p_value"
+names(output)[5] <- "adjusted_p_value"
+
+output_json <- toJSON(output)
+print ("output_json")
+output_file <- paste0(input$output_path,"/r_output.txt")
+print (output_file)
+cat(output_json, file = output_file)
+#top_degs = topTags(object = et, n = "Inf")
+#print ("top_degs")
+#print (top_degs)