data-raw/GSE74821.R

In mcanouil/NACHO: NanoString Quality Control Dashboard

#' GSE74821
library(GEOquery)
devtools::load_all(".") # library(NACHO)

gse <- GEOquery::getGEO(GEO = "GSE74821")
targets <- Biobase::pData(Biobase::phenoData(gse[[1]]))
GEOquery::getGEOSuppFiles(GEO = "GSE74821", baseDir = tempdir())
utils::untar(file.path(tempdir(), "GSE74821", "GSE74821_RAW.tar"), exdir = file.path(tempdir(), "GSE74821"))
targets$IDFILE <- list.files(path = file.path(tempdir(), "GSE74821"), pattern = ".RCC.gz$")
targets[] <- lapply(X = targets, FUN = iconv, from = "latin1", to = "ASCII")
select_cartridge <- unlist(lapply(
  X = c(
    "20111102_20111102-9741-1", "20111102_20111102-9741-2",
    "20111230_20111228-9741-2-0044", "20111230_20111228-9741-4-0044"
    ),
  FUN = grep,
  x = targets$IDFILE
))

GSE74821 <- load_rcc(
  data_directory = file.path(tempdir(), "GSE74821"),
  ssheet_csv = targets[select_cartridge, ],
  id_colname = "IDFILE",
  housekeeping_genes = NULL,
  housekeeping_predict = FALSE,
  housekeeping_norm = TRUE,
  normalisation_method = "GLM",
  n_comp = 10
)
GSE74821$data_directory <- "~/"
usethis::use_data(GSE74821, overwrite = TRUE)