initial commit

process.R

+workDir <- "/root/rdconnect"
+
+library(tidyr)
+
+fraserTsvPath <- "./Output/processed_results/aberrant_splicing/results/v29/fraser/fraser/results_per_junction.tsv"
+fraserRdsPath <- "./Output/processed_results/aberrant_splicing/datasets/savedObjects/fraser--v29/fds-object.RDS"
+
+setwd(workDir)
+
+
+# helper functions
+
+# adds assay to fraser tsv
+assayToDenormDF <- function(assayName, assay, tsv, gr, fds) {
+  df <- cbind(gr, assay)
+  sampleColIndices <- seq(dim(gr)[2]+1, dim(df)[2])
+  denorm_df <- pivot_longer(df, cols=all_of(sampleColIndices), names_to="sampleID", values_to=assayName)
+  newTsv <- merge(tsv, denorm_df, all.x=TRUE)
+  keepCols <- append(colnames(tsv), assayName)
+  newTsv[, keepCols]
+}
+
+# read original output file
+fraserTsv <- read.table(fraserTsvPath, sep="\t", header=TRUE)
+
+# read original binary files
+fds <- readRDS(fraserRdsPath)
+fds
+gr <- as.data.frame(granges(fds))
+
+# add additional assays that we are interested in to fraser tsv
+fraserTsv <- assayToDenormDF("predictedMeans_psi3", assays(fds)[["predictedMeans_psi3"]], fraserTsv, gr, fds)
+fraserTsv <- assayToDenormDF("pvaluesBetaBinomial_junction_psi3", assays(fds)[["pvaluesBetaBinomial_junction_psi3"]], fraserTsv, gr, fds)
+fraserTsv <- assayToDenormDF("junction_count", K(fds, type = 'psi3'), fraserTsv, gr, fds)
+fraserTsv <- assayToDenormDF("total_junction_count", N(fds, type = 'psi3'), fraserTsv, gr, fds)
+
+# write new tsv
+write.table(fraserTsv, sep = "\t", file = "fraser_complete_output.tsv", row.names=FALSE)
+
+
+##################
+##################
+
+
+outriderTsvPath <- "./Output/processed_results/aberrant_expression/v29/outrider/outrider/OUTRIDER_results.tsv"
+outriderRdsPath <- "./Output/processed_results/aberrant_expression/v29/outrider/outrider/ods.Rds"
+outriderTsv <- read.table(outriderTsvPath, sep="\t", header=TRUE)
+ods <- readRDS(outriderRdsPath)
+gr <- as.data.frame(granges(ods))