inst/scripts/make-data_22Q2.R

In UCLouvain-CBIO/depmap: Cancer Dependency Map Data Package

### =========================================================================
### Make 22Q2 depmap data
### -------------------------------------------------------------------------

## This scripts documents how to download and generate the data files.
## Note 1: This scipt assumes (!!!) that it is run in ./depmap/inst/scripts/ and
## saves the resulting .rda files in ./depmap/inst/data
## (e.g. *setwd(./depmap/inst/scripts/)*)
## Note 2: the Broad Institute may change the download urls for these datasets.
## If the link to one of these datasets is broken, please contact the package
## maintainer. All Depmap data can be downloaded from the API at
## https://depmap.org/portal/download/ even if the specific links may change

## load libraries
library("readr")
library("dplyr")
library("tidyr")

setwd("~/tmp/depmap/inst/scripts/")
## set environment variable to allow download from depmap website
Sys.setenv(VROOM_CONNECTION_SIZE = 500072)

##########################################
## depmap `metadata_22Q2` dataset
##########################################

### loading data (downloading .csv file from online source)
read_csv(file = "https://ndownloader.figshare.com/files/35020903"
         ) -> metadata_22Q2

#### Rename `metadata` columns to contain underscores and be in snake case
## note: "metadata_22Q2" has different columns than "metadata_22Q2"
names(metadata_22Q2)[1:29] <- c(
    "depmap_id", "cell_line_name",
    "stripped_cell_line_name", "cell_line",
    "aliases", "cosmic_id",
    "sex", "source",
    "RRID", "WTSI_master_cell_ID",
    "sample_collection_site", "primary_or_metastasis",
    "primary_disease", "subtype_disease",
    "age", "sanger_id",
    "additional_info", "lineage",
    "lineage_subtype", "lineage_sub_subtype",
    "lineage_molecular_subtype", "default_growth_pattern",
    "model_manipulation", "model_manipulation_details",
    "patient_id", "parent_depmap_id",
    "Cellosaurus_NCIt_disease", "Cellosaurus_NCIt_id",
    "Cellosaurus_issues")

    ## these columns have been moved the achilles
    # "Achilles_n_replicates", "cell_line_NNMD", "culture_medium",
    # "cas9_activity", 

    ## info from column "culture_type" has been split into the following:
    # "default_growth_pattern" "model_manipulation" "model_manipulation_details"

### saving cleaned and converted `metadata` data as .rda file
save(metadata_22Q2, file = "../eh_data/metadata_22Q2.rda",
      compress = "xz", compression_level = 9)

##########################################
## `dep_2_name_22Q2 map `depmap_id` to `cell_line`
##########################################

##  generation of `metadata` subset `dep_2_name_22Q2`
## The subset of `metadata`, `dep_2_name_Q2` is used to map `cell_line`
## and depmap_id via left_join in other depmap datasets that do not contain
## both variables. If you are generating the depmap data from scratch, you will
## need to run the following code to generate the data correctly.

### `dep_2_name` to add `depmap_id` or `cell_line` to other datasets
metadata_22Q2 %>% dplyr::select(depmap_id, cell_line) -> dep_2_name_22Q2

##########################################
## depmap `mutationCalls_22Q2` dataset
##########################################

### loading data (downloading .csv file from online source)
read_csv(file = "https://ndownloader.figshare.com/files/34989940"
         ) -> mutationCalls_22Q2

## note: "mutationCalls_22Q2" has different columns than "mutationCalls_19Q1"
## the variable "VA_WES_AC" is no longer present in this dataset, unlike
## previous releases (e.g. 19Q1)!
## In the 22Q2 release the feature, "tumor_seq_allele1" was changed to
## "alt_allele"
names(mutationCalls_22Q2)[1:32] <- c(
    "gene_name", "entrez_id",
    "ncbi_build", "chromosome",
    "start_pos", "end_pos",
    "strand", "var_class",
    "var_type", "ref_allele",
    "alt_allele", "dbSNP_RS",
    "dbSNP_val_status", "genome_change",
    "annotation_trans", "depmap_id",
    "cDNA_change", "codon_change",
    "protein_change", "is_deleterious",
    "is_tcga_hotspot", "tcga_hsCnt",
    "is_cosmic_hotspot", "cosmic_hsCnt",
    "ExAC_AF", "var_annotation",
    "CGA_WES_AC", "HC_AC",
    "RD_AC", "RNAseq_AC",
    "sanger_WES_AC", "WGS_AC")

### rearrange columns into same column format as other datasets
mutationCalls_22Q2 %>%
    dplyr::select(depmap_id, everything()) -> mutationCalls_22Q2

### saving cleaned and converted `mutationCalls` data as .rda file
save(mutationCalls_22Q2, file = "../eh_data/mutationCalls_22Q2.rda",
     compress = "xz", compression_level = 9)

##########################################
## depmap `copyNumber_22Q2` dataset
##########################################

### loading data (downloading .csv file from online source)
read_csv("https://ndownloader.figshare.com/files/34989937") -> copyNumber_22Q2

### rename column first column to "depmap_id"
names(copyNumber_22Q2)[1] <- "depmap_id"

### gather into long form on columns: `depmap_id`, `gene`, `logCopyNumber`
copyNumber_22Q2 %>%
  tidyr::gather(gene, log_copy_number, -depmap_id) -> copyNumber_22Q2_long

### mutate gene column into `gene_name` and `entrez_id`
copyNumber_22Q2_long %>%
    dplyr::mutate(
      entrez_id = gsub("&", ";", sub("\\)", "", sub("^.+ \\(", "", gene))),
      gene_name = gsub("&", ";", sub(" \\(.+\\)$", "", gene))
                  ) -> copyNumber_22Q2_long

### left_join `copyNumber` & `dep_2_name_22Q2` on `depmap_id`,
copyNumber_22Q2_long %>%
    dplyr::left_join(dep_2_name_22Q2, by = c("depmap_id" = "depmap_id")
                     ) -> copyNumber_22Q2

### rearrange columns into same column format as other datasets
copyNumber_22Q2 %>% 
  dplyr::select(depmap_id, gene, log_copy_number, entrez_id, gene_name,
                cell_line) %>%
  readr::type_convert(cols(entrez_id = "i")) -> copyNumber_22Q2

### saving cleaned and converted `copyNumber` data as .rda file
save(copyNumber_22Q2, file = "../eh_data/copyNumber_22Q2.rda",
     compress = "xz", compression_level = 9)

##########################################
## depmap `crispr_22Q2` dataset
##########################################

### loading data (downloading .csv file from online source)
read_csv(file = "https://ndownloader.figshare.com/files/34990036"
         ) -> crispr_22Q2

### rename column first column to "depmap_id"
names(crispr_22Q2)[1] <-"depmap_id"

### gather cripsr into long form with columns: `depmap_id`, `gene`, `dependency`
crispr_22Q2 %>%
  tidyr::gather(gene, dependency, -depmap_id) -> crispr_22Q2_long

### mutate gene into `gene_name` and `entrez_id`
crispr_22Q2_long %>%
    dplyr::mutate(
        entrez_id = gsub("&", ";", sub("\\)", "", sub("^.+ \\(", "", gene))),
        gene_name = gsub("&", ";", sub(" \\(.+\\)$", "", gene))
                  ) -> crispr_22Q2_long

### left_join `crispr_long` and `dep_2_name` to add `cell_line` column
crispr_22Q2_long %>%
  dplyr::left_join(dep_2_name_22Q2, by = c("depmap_id" = "depmap_id")
                   ) -> crispr_22Q2

### rearrange columns into same column format as other datasets
crispr_22Q2 %>%
  dplyr::select(depmap_id, gene, dependency, entrez_id, gene_name,
                cell_line) %>%
  readr::type_convert(cols(entrez_id = "i")) -> crispr_22Q2

### saving cleaned and converted `crispr` data as .rda file
save(crispr_22Q2, file = "../eh_data/crispr_22Q2.rda",
     compress = "xz", compression_level = 9)

##########################################
## depmap `TPM_22Q2` dataset
##########################################

### loading data (downloading .csv file from online source)
TPM_22Q2 <- read_csv(file = "https://ndownloader.figshare.com/files/34989919")

### rename column first column to "depmap_id"
names(TPM_22Q2)[1] <-"depmap_id"

### gather `TPM` into long form on columns: `depmap_id`, `gene`, `expression`
TPM_22Q2 %>%
  tidyr::gather(gene, rna_expression, -depmap_id) -> TPM_22Q2_long

### mutate gene into gene_name and entrez_id
TPM_22Q2_long %>%
    dplyr::mutate(
        entrez_id = gsub("&", ";", sub("\\)", "", sub("^.+ \\(", "", gene))),
        gene_name = gsub("&", ";", sub(" \\(.+\\)$", "", gene))
                  ) -> TPM_22Q2_long

### left_join join `TPM` and `dep_2_name_22Q2` to add `cell_line` column
TPM_22Q2_long %>%
  dplyr::left_join(dep_2_name_22Q2, by = c("depmap_id" = "depmap_id")
                   ) -> TPM_22Q2

### rearrange columns into same column format as other datasets
TPM_22Q2 %>%
    dplyr::select(depmap_id, gene, rna_expression, entrez_id, gene_name,
                  cell_line) %>%
    readr::type_convert(cols(entrez_id = "i")) -> TPM_22Q2

### saving cleaned and converted `TPM` data as .rda file
save(TPM_22Q2, file = "../eh_data/TPM_22Q2.rda", compress = "xz",
     compression_level = 9)

##########################################
## depmap `achilles_metadata_22Q2` dataset
##########################################
read_csv(file = "https://ndownloader.figshare.com/files/34989901"
         ) -> achilles_metadata

names(achilles_metadata)[1:5] <- c(
  "depmap_id", "achilles_n_replicates", "cell_line_NNMD", 
  "culture_medium", "cas9_activity")

## note: "culture_type" column was removed

achilles_metadata %>% 
  dplyr::left_join(dep_2_name_22Q2, by = "depmap_id") %>%
  dplyr::select(depmap_id, cell_line, everything()) -> achilles_metadata_22Q2

### saving cleaned and converted `metadata` data as .rda file
save(achilles_metadata_22Q2, file = "../eh_data/achilles_22Q2.rda",
      compress = "xz", compression_level = 9)