curatedPCaData: Curated Prostate Cancer Data

### Data downloading scripts for:
## GEX: Gene expression
## CNA: Copy number alteration
## MUT: Mutations
### Available platforms for extracting raw or processed data
## GEO: Gene Omnibus
## cBioPortal (query via cgdsr-package or superceded by cBioPortalData-package)
## XenoBrowser (TCGA re-processed)

### Rough pipeline:
## Download clinical data first (via download-clinical.R), and save in data-raw
## Download GEX/CNA/MUT and save in data-raw using functions via generate.R
## Create final MAE object for package export using functions via create.R
## Later, additional derivate variables are added in derive-variables.R and added as MAE slots

### Alphabetic ordering of datasets:
## - Abida et al.
## - Baca et al.
## - Barbieri et al.
## - Barwick et al.
## - Chandran et al.
## - Friedrich et al.
## - Hieronymus et al.
## - ICGC sub datasets
## - IGC
## - Kim et al.
## - Kunderfranco et al.
## - Ren et al.
## - Sun et al.
## - Taylor et al. (MSKCC)
## - TCGA
## - Wallace et al.
## - Wang et al.
## - Weiner et al.

## - Abida et al. -
# GEX PolyA (FPKM) z-score normalized relative to paired normal
gex.relz_abida <- curatedPCaData:::generate_cbioportaldata(
  "prad_su2c_2019",
  "gex"
)
save(gex.relz_abida, file = "data-raw/gex.relz_abida.RData")

# CNA (GISTIC)
cna.gistic_abida <- curatedPCaData:::generate_cbioportaldata(
  "prad_su2c_2019",
  "cna"
)
save(cna.gistic_abida, file = "data-raw/cna.gistic_abida.RData")

# Mutations
mut_abida <- curatedPCaData:::generate_cbioportaldata(
  "prad_su2c_2019",
  "mut"
)
save(mut_abida, file = "data-raw/mut_abida.RData")
# To check: Fusions separately?

# Create MAE object
mae_abida <- curatedPCaData:::create_mae(study_name = "abida")
usethis::use_data(mae_abida, overwrite = TRUE)

## - end Abida et al. -


## - Baca et al. -
# CNA (GISTIC)
cna.gistic_baca <- curatedPCaData:::generate_cbioportaldata(
  "prad_broad_2013",
  "cna"
)
save(cna.gistic_baca, file = "data-raw/cna.gistic_baca.RData")

# Mutations
mut_baca <- curatedPCaData:::generate_cbioportaldata("prad_broad_2013", "mut")
save(mut_baca, file = "data-raw/mut_baca.RData")

# Create MAE object
mae_baca <- curatedPCaData:::create_mae(study_name = "baca")
usethis::use_data(mae_baca, overwrite = TRUE)

## - end Baca et al. -


## - Barbieri et al. -
# GEX expression z-score normalized relative to paired normal
gex.relz_barbieri <- curatedPCaData:::generate_cbioportaldata(
  "prad_broad",
  "gex"
)
save(gex.relz_barbieri, file = "data-raw/gex.relz_barbieri.RData")

# CNA
# cna.gistic_barbieri <- curatedPCaData:::generate_cbioportal(
#   genes = sort(unique(curatedPCaData:::curatedPCaData_genes$hgnc_symbol)),
#   geneticProfiles="prad_broad_cna",
#   caseList="prad_broad_sequenced"
# )
cna.gistic_barbieri <- curatedPCaData:::generate_cbioportaldata("prad_broad", "cna")
save(cna.gistic_barbieri, file = "data-raw/cna.gistic_barbieri.RData")

# MUT
mut_barbieri <- curatedPCaData:::generate_cbioportaldata(
  "prad_broad",
  "mut"
)
save(mut_barbieri, file = "data-raw/mut_barbieri.RData")

# Create MAE object
mae_barbieri <- curatedPCaData:::create_mae(study_name = "barbieri")
usethis::use_data(mae_barbieri, overwrite = TRUE)

## - end Barbieri et al. -


## - Barwick et al.
# GEX: GPL5858	DASL Human Cancer Panel by Gene
gex.logq_barwick <- curatedPCaData:::generate_gex_geo(
  geo_code = "GSE18655"
)
save(gex.logq_barwick, file = "data-raw/gex.logq_barwick.RData")

# Create MAE object
mae_barwick <- curatedPCaData:::create_mae(study_name = "Barwick")
usethis::use_data(mae_barwick, overwrite = TRUE)

## - end Barwick et al. -


## - Chandran et al. (Yu et al.) -
# GEX: Multiple array types:
# - GPL92	[HG_U95B] Affymetrix Human Genome U95B Array
# - GPL93	[HG_U95C] Affymetrix Human Genome U95C Array
# - GPL8300	[HG_U95Av2] Affymetrix Human Genome U95 Version 2 Array
gex.rma_chandran <- curatedPCaData:::generate_gex_geo(
  geo_code = "GSE6919",
  pckg = "oligo",
  filter_regex = "_RAW"
)
save(gex.rma_chandran, file = "data-raw/gex.rma_chandran.RData")

# Create and save MAE object
mae_chandran <- curatedPCaData:::create_mae(study_name = "chandran")
usethis::use_data(mae_chandran, internal = FALSE, overwrite = TRUE)

# - end Chandran et al. -


## - Friedrich et al. (2020) -
# GEX: GPL26898	Agilent-058029 Custom human expression microarray (Probe Name version)
gex.logq_friedrich <- curatedPCaData:::generate_gex_geo(
  geo_code = "GSE134051",
  pckg = "limma",
  filter_regex = "_RAW",
  cleanup = FALSE
)
save(gex.logq_friedrich, file = "data-raw/gex.logq_friedrich.RData")

# Create and save MAE object
mae_friedrich <- curatedPCaData:::create_mae(study_name = "Friedrich")
usethis::use_data(mae_friedrich, internal = FALSE, overwrite = TRUE)

## - end Friedrich et al. -


## - Hieronymus et al. -
# CNA logr
# cna.logr_hieronymus <- curatedPCaData:::generate_cna_geo(
#   geo_code = "GSE54691"
# )
# save(cna.logr_hieronymus, file="data-raw/cna.logr_hieronymus.RData")

# CNA Gistic
cna.gistic_hieronymus <- curatedPCaData:::generate_cbioportaldata("prad_mskcc_2014", "cna")
save(cna.gistic_hieronymus, file = "data-raw/cna.gistic_hieronymus.RData")

# Create MAE object
mae_hieronymus <- curatedPCaData:::create_mae(study_name = "hieronymus")
usethis::use_data(mae_hieronymus, internal = FALSE, overwrite = TRUE)

## - end Hieronymus et al. -


## - ICGC datasets -

# PRAD-CA
# Affymetrix Human Gene 1.0 ST
gex.rma_icgcca <- curatedPCaData:::generate_icgc("PRAD_CA", "gex")
save(gex.rma_icgcca, file = "data-raw/gex.rma_icgcca.RData")

# TODO: Copy-number alterations, mutations (available in ICGC)

# Create MAE object
mae_icgcca <- curatedPCaData:::create_mae(study_name = "icgcca")
usethis::use_data(mae_icgcca, internal = FALSE, overwrite = TRUE)



# PRAD-FR
gex_icgcfr <- curatedPCaData::generate_icgc("PRAD_FR", "gex")
save(gex_icgcfr, file = "data-raw/gex_icgcfr.RData")

# TODO: At this point the data contains raw read counts, and is not yet usable as a 2-dim gex matrix

# TODO: MAE

# PRAD-UK

# Only contains CNA data

## - end ICGC datatasets -



## - IGC -
# GEX: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
gex.rma_igc <- curatedPCaData:::generate_gex_geo(
  geo_code = "GSE2109",
  cleanup = FALSE,
  # Do not download the batch files, filter the raw dump and filter down to prostate specific samples afterwards
  filter_regex = "_RAW",
)
save(gex.rma_igc, file = "data-raw/gex.rma_igc.RData")

# Create MAE object
mae_igc <- curatedPCaData:::create_mae(study_name = "igc")
usethis::use_data(mae_igc, overwrite = TRUE)

## - end IGC -


## - Kim et al. -
# GEX: [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version]
gex.rma_kim <- curatedPCaData:::generate_gex_geo(
  geo_code = "GSE119616",
  pckg = "oligo",
  cleanup = FALSE
)
save(gex.rma_kim, file = "data-raw/gex.rma_kim.RData")

# Create MAE object
mae_kim <- curatedPCaData:::create_mae(study_name = "kim")
usethis::use_data(mae_kim, overwrite = TRUE)

## - end Kim et al. -


## - Kunderfranco et al. -
# GEX: Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version)
# Global LOESS normalized log ratios between the two colour arrays combined by mean with flipped dye swap
gex.logr_kunderfranco <- curatedPCaData:::generate_gex_geo(
  geo_code = "GSE14206",
  pckg = "limma",
  cleanup = FALSE
)
save(gex.logr_kunderfranco, file = "data-raw/gex.logr_kunderfranco.RData")

# Create MAE object
mae_kunderfranco <- curatedPCaData:::create_mae(study_name = "kunderfranco")
usethis::use_data(mae_kunderfranco, internal = FALSE, overwrite = TRUE)

## - end Kunderfranco et al. -



## - Ren et al. -
# GEX
# gex.relz_ren <- curatedPCaData:::generate_cbioportal(
#   genes = sort(unique(curatedPCaData:::curatedPCaData_genes$hgnc_symbol)), # All unique gene symbols
#   geneticProfiles = "prad_eururol_2017_rna_seq_mrna", # Omics profile
#   caseList = "prad_eururol_2017_sequenced" # Case list
# )
gex.relz_ren <- curatedPCaData:::generate_cbioportaldata("prad_eururol_2017", "gex")
save(gex.relz_ren, file = "data-raw/gex.relz_ren.RData")

# CNA
cna.gistic_ren <- curatedPCaData:::generate_cbioportaldata(
  "prad_eururol_2017",
  "cna"
)
save(cna.gistic_ren, file = "data-raw/cna.gistic_ren.RData")

# Mutations
mut_ren <- curatedPCaData:::generate_cbioportaldata(
  "prad_eururol_2017",
  "mut"
)
save(mut_ren, file = "data-raw/mut_ren.RData")

# Create MAE object
mae_ren <- curatedPCaData:::create_mae(study_name = "ren")
usethis::use_data(mae_ren, overwrite = TRUE)

## - end Ren et al.


## - Sun et al.  -
# GEX: [HG-U133A] Affymetrix Human Genome U133A Array
gex.rma_sun <- curatedPCaData:::generate_gex_geo(
  geo_code = "GSE25136",
  cleanup = FALSE,
  pckg = "oligo"
)
save(gex.rma_sun, file = "data-raw/gex.rma_sun.RData")

# Create MAE object
mae_sun <- curatedPCaData:::create_mae(study_name = "Sun")
usethis::use_data(mae_sun, overwrite = TRUE)

## - end Sun et al. -


## Taylor et al., also known as the MSKCC data -----
# GEX:
# - GPL5188	[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version]
# - GPL8227	Agilent-019118 Human miRNA Microarray 2.0 G4470B (miRNA ID version)
# - GPL10264	Affymetrix Human Exon 1.0 ST Array [CDF: HuEx_1_0_st_v2_main_A20071112_EP.cdf]
gex.rma_taylor <- curatedPCaData:::generate_gex_geo(
  geo_code = "GSE21032",
  cleanup = FALSE,
  pckg = "oligo"
)
save(gex.rma_taylor, file = "data-raw/gex.rma_taylor.RData")

# CNA (Log-ratios)
cna.logr_taylor <- curatedPCaData:::generate_cna_geo(
  geo_code = "GSE21035"
)
save(cna.logr_taylor, file = "data-raw/cna.logr_taylor.RData")

# CNA (GISTIC)
cna.gistic_taylor <- curatedPCaData:::generate_cbioportaldata(
  "prad_mskcc", "cna"
)
save(cna.gistic_taylor, file = "data-raw/cna.gistic_taylor.RData")

# Mutations
mut_taylor <- curatedPCaData:::generate_cbioportaldata("prad_mskcc", "mut")
save(mut_taylor, file = "data-raw/mut_taylor.RData")

# Create MAE object
mae_taylor <- curatedPCaData:::create_mae(study_name = "Taylor")
usethis::use_data(mae_taylor, overwrite = TRUE)

## - end Taylor et al. (MSKCC) -


## - TCGA -
# GEX
gex.rsem.log_tcga <- curatedPCaData:::generate_xenabrowser(
  id = "TCGA-PRAD",
  type = "gex",
  digits = 4,
  truncate = 0 # '.01A' -> '.01' suffix
)
save(gex.rsem.log_tcga, file = "data-raw/gex.rsem.log_tcga.RData")

# CNA (GISTIC)
cna.gistic_tcga <- curatedPCaData:::generate_xenabrowser(
  id = "TCGA-PRAD",
  type = "cna",
  truncate = 0 # '.01A' -> '.01' suffix
)
save(cna.gistic_tcga, file = "data-raw/cna.gistic_tcga.RData")

# Mutations
mut_tcga <- curatedPCaData:::generate_xenabrowser(
  id = "TCGA-PRAD",
  type = "mut",
  truncate = 0 # '.01A' -> '.01' suffix
)
save(mut_tcga, file = "data-raw/mut_tcga.RData")

# Create MAE object
mae_tcga <- curatedPCaData:::create_mae(study_name = "TCGA")
usethis::use_data(mae_tcga, overwrite = TRUE)

## - end TCGA -

## - True et al. -
# GEX:
# 	GPL3834	FHCRC Human Prostate PEDB cDNA Array v4
# 	GPL3836	FHCRC Human Prostate PEDB cDNA Array v3 (-> single sample only! 11th, GSM115769)
gex.logr_true <- curatedPCaData:::generate_gex_geo(
  geo_code = "GSE5132",
  pckg = "limma",
  cleanup = FALSE,
  filter_regex = "_RAW"
)
save(gex.logr_true, file = "data-raw/gex.logr_true.RData")

# Create MAE object
mae_true <- curatedPCaData:::create_mae(study_name = "true")
usethis::use_data(mae_true, internal = FALSE, overwrite = TRUE)

## - end True et al. -


## - Wallace et al. -
# GEX: [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array
gex.rma_wallace <- curatedPCaData:::generate_gex_geo(
  geo_code = "GSE6956",
  pckg = "oligo",
  cleanup = FALSE
)
save(gex.rma_wallace, file = "data-raw/gex.rma_wallace.RData")

# Create and save MAE object
mae_wallace <- curatedPCaData:::create_mae(study_name = "wallace")
usethis::use_data(mae_wallace, internal = FALSE, overwrite = TRUE)

## - end Wallace et al. -


# - Wang et al. -
# GEX: [HG-U133A] Affymetrix Human Genome U133A Array
gex.rma_wang <- curatedPCaData:::generate_gex_geo(
  geo_code = "GSE8218",
  pckg = "oligo"
)
save(gex.rma_wang, file = "data-raw/gex.rma_wang.RData")

## CNA
# cna_wang <- curatedPCaData:::generate_cna_geo(
#  geo_code = "GSE8218"
# )
# save(cna_wang, file="data-raw/cna_wang.RData")

# Create MAE object
mae_wang <- curatedPCaData:::create_mae(study_name = "wang")
usethis::use_data(mae_wang, overwrite = TRUE)

# - end Wang et al. -


# - Weiner et al. -
# GEX: GPL5175	[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]
gex.rma_weiner <- curatedPCaData:::generate_gex_geo(
  geo_code = "GSE157548",
  pckg = "oligo"
)
save(gex.rma_weiner, file = "data-raw/gex.rma_weiner.RData")

# Create MAE object
mae_weiner <- curatedPCaData:::create_mae(study_name = "weiner")
usethis::use_data(mae_weiner, overwrite = TRUE)

# - end Weiner et al. -