Add GTEx tissues dataset

R/data.R

@@ -4,6 +4,9 @@
 #' The results from the analysis across all GTEx samples.
 "gtex_all"
 
+#' The results from the analysis across GTEx tissue aggregated data.
+"gtex_tissues"
+
 #' The results from the analysis across Human Protein Atlas' tissue aggregated
 #' data.
 "hpa_tissues"

R/server.R

@@ -2,7 +2,9 @@
 #' @noRd
 server <- function(input, output, session) {
   dataset <- reactive({
-    analysis <- if (input$dataset == "hpa_tissues") {
+    analysis <- if (input$dataset == "gtex_tissues") {
+      ubigen::gtex_tissues
+    } else if (input$dataset == "hpa_tissues") {
       ubigen::hpa_tissues
     } else {
       ubigen::gtex_all

R/ui.R

@@ -23,8 +23,9 @@ ui <- function() {
               "dataset",
               label = strong("Expression dataset"),
               list(
-                "GTEx (all samples)" = "gtex_all",
-                "Human Protein Atlas (tissues)" = "hpa_tissues"
+                "GTEx (across tissues and conditions)" = "gtex_all",
+                "GTEx (across tissues)" = "gtex_tissues",
+                "Human Protein Atlas (across tissues)" = "hpa_tissues"
               )
             ),
             selectInput(

man/gtex_tissues.Rd

@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{gtex_tissues}
+\alias{gtex_tissues}
+\title{The results from the analysis across GTEx tissue aggregated data.}
+\format{
+An object of class \code{data.table} (inherits from \code{data.frame}) with 56156 rows and 17 columns.
+}
+\usage{
+gtex_tissues
+}
+\description{
+The results from the analysis across GTEx tissue aggregated data.
+}
+\keyword{datasets}

scripts/gtex_tissues.R

@@ -0,0 +1,23 @@
+library(data.table)
+library(here)
+
+i_am("scripts/gtex_tissues.R")
+
+# Source: https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct.gz
+data <- fread(here("scripts", "input", "gtex_tissues.tsv"))
+data[, Description := NULL]
+setnames(data, "Name", "gene")
+
+# Remove Ensembl gene version numbers.
+data[, gene := stringr::str_split(gene, "\\.") |> purrr::map_chr(1)]
+
+data <- melt(
+    data,
+    id.vars = "gene",
+    variable.name = "sample",
+    value.name = "expression",
+    variable.factor = FALSE
+)
+
+gtex_tissues <- ubigen::analyze(data)
+usethis::use_data(gtex_tissues, overwrite = TRUE)

scripts/hpa_tissues.R

@@ -1,7 +1,7 @@
 library(data.table)
 library(here)
 
-i_am("scripts/hpa.R")
+i_am("scripts/hpa_tissues.R")
 
 # Source: https://www.proteinatlas.org/download/rna_tissue_hpa.tsv.zip
 data <- fread(here("scripts", "input", "rna_tissue_hpa.tsv"))