diff --git a/R/data.R b/R/data.R index 807fe75..4ace068 100644 --- a/R/data.R +++ b/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" diff --git a/R/server.R b/R/server.R index 04c703b..bfe51e0 100644 --- a/R/server.R +++ b/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 diff --git a/R/ui.R b/R/ui.R index ba781d7..56cafdc 100644 --- a/R/ui.R +++ b/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( diff --git a/data/gtex_tissues.rda b/data/gtex_tissues.rda new file mode 100644 index 0000000..1e3da18 Binary files /dev/null and b/data/gtex_tissues.rda differ diff --git a/man/gtex_tissues.Rd b/man/gtex_tissues.Rd new file mode 100644 index 0000000..048d258 --- /dev/null +++ b/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} diff --git a/scripts/gtex_tissues.R b/scripts/gtex_tissues.R new file mode 100644 index 0000000..dea1a49 --- /dev/null +++ b/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) diff --git a/scripts/hpa.R b/scripts/hpa_tissues.R similarity index 81% rename from scripts/hpa.R rename to scripts/hpa_tissues.R index 18f99fc..900a2e5 100644 --- a/scripts/hpa.R +++ b/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"))