Initial commit -- code as run on initial submission.

JRT_preprocess.R

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+#JRT 22May2020
+#Input files downloaded from Omicsoft result folders for each project
+#P-20170104-0001_Scleroderma_RNA-Seq.QCMetrics.txt
+#P-20170104-0001_Lung_RNA-Seq.QCMetrics.txt
+#Summarize QC stats 
+#was read length, insert size distribution and other technical details about the RNA-seq
+#
+## ReadLength = 75bp PE 
+## Library Pre  = TruSeq Stranded Total RNA Ribo Zero-Gold
+## Genome = Mouse.B38
+## Gene Model = Ensembl.R86
+## 
+
+library(magrittr)
+library(tidyverse)
+library(DGEobj)
+library(DGE.Tools2)
+library(JRTutil)
+library(matrixStats)
+
+qc_skin <- read_delim("P-20170104-0001_Scleroderma_RNA-Seq.QCMetrics.txt", delim="\t")
+qc_lung <- read_delim("P-20170104-0001_Lung_RNA-Seq.QCMetrics.txt", delim="\t")
+#print available metrics
+qc$Metric
+
+metricNames= c("Alignment_All", "Alignment_MappedRate", "Alignment_PairedRate",
+               "Alignment_UniquelyMappedRate","InsertSize_Median", "InsertSize_Mean",
+               "Profile_ExonRate", "Profile_IntronRate", "Profile_InterGeneRate",
+               "Profile_InterGene_FPK", "Source_antisenseRate", "Source_MitochondrialRate")
+
+skinPlots <- QCplots(qc_skin,
+        sampleNames = as.character(1:(ncol(qc_skin)-1)),
+        metricNames= metricNames)
+for (metric in names(skinPlots)){
+  ggsave(str_c("skin_", metric, ".png"), skinPlots[[metric]])
+}
+
+qcstats_skin <- qc_skin
+qcstats_skin$mean <- rowMeans(qc_skin[,2:ncol(qc_skin)])
+qcstats_skin$sd <- rowSds(as.matrix(qc_skin[,2:ncol(qc_skin)]))
+qcstats_skin$min <- rowMins(as.matrix(qc_skin[,2:ncol(qc_skin)]))
+qcstats_skin$max <- rowMaxs(as.matrix(qc_skin[,2:ncol(qc_skin)]))
+qcstats_skin[,2:ncol(qc_skin)] <- NULL
+#just the metrics selected
+idx <- qcstats_skin$Metric %in% metricNames
+qcstats_skin <- qcstats_skin[idx,]
+write_delim(qcstats_skin, path="qcstats_skin.txt", delim = "\t")
+
+###  Now same for lung
+lungPlots <- QCplots(qc_lung,
+        sampleNames = as.character(1:(ncol(qc_lung)-1)),
+        metricNames= metricNames)
+
+for (metric in names(lungPlots)){
+  ggsave(str_c("lung_", metric, ".png"), skinPlots[[metric]])
+}
+
+qcstats_lung <- qc_lung
+qcstats_lung$mean <- rowMeans(qc_lung[,2:ncol(qc_lung)])
+qcstats_lung$sd <- rowSds(as.matrix(qc_lung[,2:ncol(qc_lung)]))
+qcstats_lung$min <- rowMins(as.matrix(qc_lung[,2:ncol(qc_lung)]))
+qcstats_lung$max <- rowMaxs(as.matrix(qc_lung[,2:ncol(qc_lung)]))
+qcstats_lung[,2:ncol(qc_lung)] <- NULL
+#just the metrics selected
+idx <- qcstats_lung$Metric %in% metricNames
+qcstats_lung <- qcstats_lung[idx,]
+write_delim(qcstats_lung, path="qcstats_lung.txt", delim = "\t")