_annotation-file-generator.R

# ####################################
# Create an up-to-date annotation file
# ####################################

# Install required packages
if (!require('BiocManager', quietly = TRUE))
  install.packages('BiocManager')

BiocManager::install('biomaRt', update = TRUE, ask = FALSE, checkBuilt = TRUE)

require(biomaRt)

# Get annotation table
ensembl <- useEnsembl(biomart = 'genes', dataset = 'hsapiens_gene_ensembl')

annotLookup <- getBM(
  mart = ensembl,
  attributes = c(
    'agilent_sureprint_g3_ge_8x60k_v2',
    'ensembl_gene_id',
    'external_gene_name'
  )
)

# Export annotation table as tsv file
today <- format(Sys.Date(), format='%Y-%m')

write.table(
  annotLookup,
  paste0('Human_agilent_sureprint_g3_ge_8x60k_v2_', gsub('-', '_', as.character(today)), '.tsv'),
  sep = '\t',
  row.names = FALSE,
  quote = FALSE
)