inst/extdata/process.R

In aeolianine/CRCsubtyping: Subtyping Colorectal Expression Data

# This is a collection of data processing scripts, used to store the
# gene signatures from publications as data in this package.

process_inmf_sigs_from_supplement = FALSE

if (process_inmf_sigs_from_supplement){
  # iNMF gene signature stored as entrez identifiers
  # source: https://bmcmedgenomics.biomedcentral.com/articles/10.1186/1755-8794-5-66

  t1 = scan('12920_2012_343_MOESM2_ESM_entrez.txt', sep = '\t', skip=1)
  t2 = scan('12920_2012_343_MOESM3_ESM_entrez.txt', sep = '\t', skip=1)
  t1.1 = scan('12920_2012_343_MOESM4_ESM_entrez.txt', sep = '\t', skip=1)
  t1.2 = scan('12920_2012_343_MOESM5_ESM_entrez.txt', sep = '\t', skip=1)
  t1.3 = scan('12920_2012_343_MOESM6_ESM_entrez.txt', sep = '\t', skip=1)
  t2.1 = scan('12920_2012_343_MOESM7_ESM_entrez.txt', sep = '\t', skip=1)
  t2.2 = scan('12920_2012_343_MOESM8_ESM_entrez.txt', sep = '\t', skip=1)

  inmf_signatures_entrez = list()
  inmf_signatures_entrez[['1']] = t1
  inmf_signatures_entrez[['2']] = t2
  inmf_signatures_entrez[['1.1']] = t1.1
  inmf_signatures_entrez[['1.2']] = t1.2
  inmf_signatures_entrez[['1.3']] = t1.3
  inmf_signatures_entrez[['2.1']] = t2.1
  inmf_signatures_entrez[['2.2']] = t2.2

  library(devtools)
  devtools::use_data(inmf_signatures_entrez, overwrite=TRUE)

  # TODO: is this actually needed?
  file.rename('inmf_signatures_entrez.rda', '../../data/inmf_signatures_entrez.rda')

  remove(inmf_signatures_entrez, t1, t2, t1.1, t1.2, t1.3, t2.1, t2.2)
}


save_inmf_symbol_signature_to_package_data = FALSE

if (save_inmf_symbol_signature_to_package_data){
  # iNMF gene signature stored as gene symbols

  # This data file was obtained by converting the entrez id's to gene symbols by Schlicker and colleages.
  # It is shared as obtained and used in the original paper. Quote from paper:
  #      "The mapping of probe sets to ENTREZ gene identifiers, gene symbols, and KEGG [39] pathways
  #       was done using the hgu133plus2.db package (version 2.7.1)."

  load("inmf_signatures_sym.rdata")

  inmf_signatures_sym = list()
  inmf_signatures_sym[['1']] = ts.az.clust1.sym
  inmf_signatures_sym[['2']] = ts.az.clust2.sym
  inmf_signatures_sym[['1.1']] = ts.az.clust1.1.sym
  inmf_signatures_sym[['1.2']] = ts.az.clust1.2.sym
  inmf_signatures_sym[['1.3']] = ts.az.clust1.3.sym
  inmf_signatures_sym[['2.1']] = ts.az.clust2.1.sym
  inmf_signatures_sym[['2.2']] = ts.az.clust2.2.sym


  devtools::use_data(inmf_signatures_sym, overwrite=TRUE)
  # TODO: is this actually needed?
  file.rename('inmf_signatures_sym.rda', '../../data/inmf_signatures_sym.rda')

  # clean up
  remove(inmf_signatures_sym, ts.az.clust1.sym, ts.az.clust2.sym, ts.az.clust1.1.sym, ts.az.clust1.2.sym,
		 ts.az.clust1.3.sym, ts.az.clust2.1.sym, ts.az.clust2.2.sym)
}

process_Sadanandam_gene_signature = FALSE

if (process_Sadanandam_gene_signature){
  # Sadanandam gene signature, and centroids
  # source: https://images.nature.com/original/nature-assets/nm/journal/v19/n5/extref/nm.3175-S2.xls

  t = read.delim('Sadanandam786genes.csv', sep = ';', skip=6, header = TRUE)
  rownames(t) = t[, 'Genes']
  t = t[, -1]

  sadanandam_786_genes = t
  devtools::use_data(sadanandam_786_genes, overwrite=TRUE)
  file.rename('sadanandam_786_genes.rda', '../../data/sadanandam_786_genes.rda')

  remove(t, sadanandam_786_genes)

}