data-raw/data-curatedPCaData_genes.R

In Syksy/curatedPCaData: Curated Prostate Cancer Data

# Bioconductor;
# Warning! Old packages may cause some dependencies to fail, while their updating may fail if they're already in use for the session
# Safest is to update all Bioconductor packages before analyses / running pipelines

# BioConductor 'annotate' package for all sorts of conversions and genetic location info, etc
# Annotation for microarrays
# For Entrez <-> Hugo Gene Symbol mapping
# http://bioconductor.org/packages/release/bioc/html/annotate.html

# Genome wide annotation for Human
# For Entrez <-> Hugo Gene Symbol mapping (database)
# https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html

# See if legacy aliases are supported
# grep("alias", biomaRt::listAttributes(biomaRt::useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl"))[,"name"], value=TRUE)

# Example for extracting the affy specific probes as suggested in https://www.biostars.org/p/402677/
# mart <- biomaRt::useMart("ENSEMBL_MART_ENSEMBL")
# mart <- biomaRt::useDataset(grep("hsapiens", listDatasets(mart)[,1], value=TRUE), mart)
# listAttributes(mart)[grep("affy", listAttributes(mart)[,1]),]
# listAttributes(mart)[grep("agilent", listAttributes(mart)[,1]),]
#> listAttributes(mart)[grep("affy", listAttributes(mart)[,1]),]
#                     name                 description         page
# 107          affy_hc_g110          AFFY HC G110 probe feature_page
# 108         affy_hg_focus         AFFY HG Focus probe feature_page
# 109         affy_hg_u133a         AFFY HG U133A probe feature_page
# 110       affy_hg_u133a_2       AFFY HG U133A 2 probe feature_page
# 111         affy_hg_u133b         AFFY HG U133B probe feature_page
# 112   affy_hg_u133_plus_2   AFFY HG U133 Plus 2 probe feature_page
# 113          affy_hg_u95a          AFFY HG U95A probe feature_page
# 114        affy_hg_u95av2        AFFY HG U95Av2 probe feature_page
# 115          affy_hg_u95b          AFFY HG U95B probe feature_page
# 116          affy_hg_u95c          AFFY HG U95C probe feature_page
# 117          affy_hg_u95d          AFFY HG U95D probe feature_page
# 118          affy_hg_u95e          AFFY HG U95E probe feature_page
# 119          affy_hta_2_0          AFFY HTA 2 0 probe feature_page
# 120   affy_huex_1_0_st_v2   AFFY HuEx 1 0 st v2 probe feature_page
# 121         affy_hugenefl         AFFY HuGeneFL probe feature_page
# 122 affy_hugene_1_0_st_v1 AFFY HuGene 1 0 st v1 probe feature_page
# 123 affy_hugene_2_0_st_v1 AFFY HuGene 2 0 st v1 probe feature_page
# 124        affy_primeview        AFFY PrimeView probe feature_page
# 125         affy_u133_x3p         AFFY U133 X3P probe feature_page
#> listAttributes(mart)[grep("agilent", listAttributes(mart)[,1]),]
#                                name                            description         page
# 126                  agilent_cgh_44b                  AGILENT CGH 44b probe feature_page
# 127                 agilent_gpl26966                 AGILENT GPL26966 probe feature_page
# 128                  agilent_gpl6848                  AGILENT GPL6848 probe feature_page
# 129    agilent_sureprint_g3_ge_8x60k    AGILENT SurePrint G3 GE 8x60k probe feature_page
# 130 agilent_sureprint_g3_ge_8x60k_v2 AGILENT SurePrint G3 GE 8x60k v2 probe feature_page
# 131              agilent_wholegenome              AGILENT WholeGenome probe feature_page
# 132     agilent_wholegenome_4x44k_v1     AGILENT WholeGenome 4x44k v1 probe feature_page
# 133     agilent_wholegenome_4x44k_v2     AGILENT WholeGenome 4x44k v2 probe feature_page

# If main Ensembl is unresponsive, specific mirror can be specified:
# mart <- biomaRt::useEnsembl(biomart = "ensembl", mirror = "uswest", dataset="hsapiens_gene_ensembl")
mart <- biomaRt::useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
# Fetch gene names for various annotations

###
#
# Generic gene annotations
#
###

# Gene type annotations
curatedPCaData_genes <- biomaRt::getBM(
  attributes =
    c(
      # Hugo
      "hgnc_symbol",
      # Entrez gene IDs
      "entrezgene_id",
      # ENSEMBL
      "ensembl_gene_id", "ensembl_transcript_id",
      # RefSeq
      "refseq_mrna",
      # Chromosomal information
      "chromosome_name", "start_position", "end_position",
      # For identifying protein coding regions
      "transcript_biotype" # ,
      # Description
      #' description'
    ),
  mart = mart
)

###
#
# Array specific annotation sets; most popular array types for convenience
#
###

# Affymetrix HG U133A
# curatedPCaData_genes_affy_hg_u133a <- biomaRt::getBM(
# 	attributes =
# 		c(
# 			# Hugo
# 			'hgnc_symbol',
# 			# Affymetrix HG U133A
# 			'affy_hg_u133a'
# 		),
# 	mart = mart
# )
# Affymetrix HG U133A v2
# curatedPCaData_genes_affy_hg_u133a_2 <- biomaRt::getBM(
# 	attributes =
# 		c(
# 			# Hugo
# 			'hgnc_symbol',
# 			# Affymetrix HG U133A v2
# 			'affy_hg_u133a_2'
# 		),
# 	mart = mart
# )

# Sort the generic list first using chromosomes and then bp locations
curatedPCaData_genes <- curatedPCaData_genes[order(curatedPCaData_genes$chromosome_name, curatedPCaData_genes$start_position, curatedPCaData_genes$end_position), ]
# Connect to annotation database and extract a list of gene name synonyms, aliases, legacy names
db.con <- org.Hs.eg.db::org.Hs.eg_dbconn()
# SQL query
aliases <- DBI::dbGetQuery(db.con, "SELECT * FROM alias, gene_info WHERE alias._id == gene_info._id;")
curatedPCaData_genes[, "Aliases"] <- unlist(lapply(curatedPCaData_genes$hgnc_symbol, FUN = function(g) {
  w <- which(aliases[, "symbol"] == g)
  if (length(w) > 0) {
    paste0(aliases[w, "alias_symbol"], collapse = ";")
  } else {
    ""
  }
}))
# Omit row names (wrong order indices)
rownames(curatedPCaData_genes) <- NULL
# Save gene information extraction date as an attribute 'date' to all gene annotation objects for versioning purposes
attr(curatedPCaData_genes, "date") <- Sys.time()
# attr(curatedPCaData_genes_affy_hg_u133a, 'date') <- Sys.time()
# attr(curatedPCaData_genes_affy_hg_u133a_2, 'date') <- Sys.time()
# Save the time stamped gene level data
usethis::use_data(
  # Save the list of genes and metadata
  curatedPCaData_genes,
  # Array specific annotations
  # curatedPCaData_genes_affy_hg_u133a,
  # curatedPCaData_genes_affy_hg_u133a_2,
  # Saving parameters
  internal = TRUE, overwrite = TRUE, compress = "xz"
)