ubigen/scripts/hpa_tissues.R

library(data.table)
library(here)

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"))
setnames(data, c("Gene", "Tissue", "nTPM"), c("gene", "sample", "expression"))
data[, `:=`("Gene name" = NULL, TPM = NULL, pTPM = NULL)]

hpa_tissues <- ubigen::analyze(data)
usethis::use_data(hpa_tissues, overwrite = TRUE)
Allow selecting the expression dataset 2022-12-01 21:23:46 +01:00			`library(data.table)`
			`library(here)`

Add GTEx tissues dataset 2022-12-01 21:34:07 +01:00			`i_am("scripts/hpa_tissues.R")`
Allow selecting the expression dataset 2022-12-01 21:23:46 +01:00
			`# Source: https://www.proteinatlas.org/download/rna_tissue_hpa.tsv.zip`
			`data <- fread(here("scripts", "input", "rna_tissue_hpa.tsv"))`
			`setnames(data, c("Gene", "Tissue", "nTPM"), c("gene", "sample", "expression"))`
			data[, `:=`("Gene name" = NULL, TPM = NULL, pTPM = NULL)]

			`hpa_tissues <- ubigen::analyze(data)`
			`usethis::use_data(hpa_tissues, overwrite = TRUE)`