vignettes/load_dsgraveley2011.R

In LBMC/RAPToR: Real Age Prediction from Transcriptome staging On Reference

g_url_dsgraveley2011 <- paste0(
  "ftp://ftp.fruitfly.org/pub/download/modencode_expression_scores/",
  "Celniker_Drosophila_Annotation_20120616_1428_allsamps_",
  "MEAN_gene_expression.csv.gz")
g_file_dsgraveley2011 <- paste0(data_folder, "dsgraveley2011.csv.gz")
utils::download.file(g_url_dsgraveley2011, destfile = g_file_dsgraveley2011)


X_dsgraveley2011 <- read.table(gzfile(g_file_dsgraveley2011), 
                               sep = ',', row.names = 1, h = T)

# convert gene ids to FBgn
X_dsgraveley2011 <- RAPToR::format_ids(X_dsgraveley2011, droso_genes, 
                                       from = "gene_name", to = "fb_id")

# select embryo time series samples
X_dsgraveley2011 <- X_dsgraveley2011[,1:12]

P_dsgraveley2011 <- data.frame(
  sname = colnames(X_dsgraveley2011),
  age = as.numeric(gsub("em(\\d+)\\.\\d+hr", "\\1",
                        colnames(X_dsgraveley2011))),
  stringsAsFactors = FALSE)

dsgraveley2011 <- list(g = X_dsgraveley2011, p = P_dsgraveley2011)

save(dsgraveley2011, 
     file = paste0(data_folder, "dsgraveley2011.RData"), compress = "xz")

# cleanup
file.remove(g_file_dsgraveley2011)
rm(g_url_dsgraveley2011, g_file_dsgraveley2011, 
   X_dsgraveley2011, P_dsgraveley2011)