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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| #' Get OpenTargets | ||
| #' | ||
| #' Get OpenTargets disease-gene associations data | ||
| #' @source \href{https://community.opentargets.org/t/r-script-for-graphql-query-query-targetdiseaseevidence/662/5}{OpenTargets GraphQL queries in R} | ||
| #' @import rvest | ||
| #' @export | ||
| #' @examples | ||
| #' d <- get_opentargets() | ||
| get_opentargets <- function(release="latest", | ||
| data_type=c("associationByDatasourceDirect", | ||
| "associationByDatasourceIndirect", | ||
|
|
||
| "associationByDatatypeDirect", | ||
| "associationByDatatypeIndirect", | ||
|
|
||
| "associationByOverallDirect", | ||
| "associationByOverallIndirect" | ||
| )[1], | ||
| server="https://ftp.ebi.ac.uk/pub/databases/opentargets/", | ||
| subdir=c("platform/","genetics/")[1], | ||
| subdir2=c("/output/etl/parquet/","/")[1], | ||
| ftp = paste0(server, | ||
| subdir, | ||
| release, | ||
| subdir2, | ||
| data_type[1],"/"), | ||
| save_dir=cache_dir(), | ||
| force_new=FALSE){ | ||
|
|
||
| ## Variant and gene level data merged for all genome-wide summary statistics: | ||
| # ftp="https://ftp.ebi.ac.uk/pub/databases/opentargets/genetics/latest/d2v2g_scored/" | ||
| save_path <- file.path(save_dir, | ||
| paste0("opentargets_",data_type,".rds")) | ||
| #### Import cached data #### | ||
| if(file.exists(save_path) && | ||
| isFALSE(force_new)){ | ||
| messager("Loading cached file -->",save_path) | ||
| return(readRDS(save_path)) | ||
| } | ||
| #### Get new data #### | ||
| requireNamespace("arrow") | ||
| #### Scrape FTP to get file names #### | ||
| tbl <- ( | ||
| rvest::read_html(ftp)|> | ||
| rvest::html_table() | ||
| )[[1]]|> | ||
| subset(endsWith(Name,".parquet")|endsWith(Name,".json")) | ||
| tbl$Date <- stringr::str_split(tbl$`Last modified`," ",simplify = TRUE)[,1] | ||
| if(nrow(tbl)==0) stopper("No data files found at", ftp) | ||
| BPPARAM <- set_cores() | ||
| d <- BiocParallel::bplapply(stats::setNames(tbl$Name, | ||
| tbl$Name), | ||
| BPPARAM = BPPARAM, | ||
| function(f){ | ||
|
|
||
| if(endsWith(f,".json")){ | ||
| j <- jsonlite::fromJSON(file.path(ftp, f)) | ||
| jsonlite::fromJSON(j$serialisedSchema) | ||
| } else if (endsWith(f,".parquet")){ | ||
| arrow::read_parquet(file.path(ftp, f)) |> | ||
| data.table::data.table() | ||
| } | ||
| }) |> data.table::rbindlist(idcol = "file") | ||
| attr(d,"version") <- tbl$Date[[1]] | ||
| #### Report #### | ||
| messager("OpenTargets data loaded with:", | ||
| "\n-",formatC(nrow(d), big.mark = ","),"rows", | ||
| if("targetId" %in% names(d)){ | ||
| paste("\n-",formatC(length(unique(d$targetId)), big.mark = ","), | ||
| "unique targets across" ) | ||
| }, | ||
| if("diseaseId" %in% names(d)){ | ||
| paste("\n-",formatC(length(unique(d$diseaseId)), big.mark = ","), | ||
| "unique diseases across" ) | ||
| }, | ||
| v = TRUE) | ||
| cache_save(d, save_path) | ||
| return(d) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,10 +1,7 @@ | ||
| #' @describeIn query_ query_ | ||
| #' @inheritDotParams monarchr::biolink_search | ||
| #' @export | ||
| #' @examples | ||
| #' cells <- monarchr::biolink_search(phrase_or_id = "T-cell") | ||
| query_monarch <- function(...){ | ||
| requireNamespace("monarchr") | ||
| monarchr::biolink_search(...) | ||
| # monarchr::biolink_search(...) | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| #' Set cores | ||
| #' | ||
| #' Assign cores automatically for parallel processing, while reserving some. | ||
| #' | ||
| #' @param workers Number (>1) or proportion (<1) of worker cores to use. | ||
| #' @param verbose Print messages. | ||
| #' @param progressbar logical(1) Enable progress bar | ||
| #' (based on \code{plyr:::progress_text}). | ||
| #' Enabling the progress bar changes the default value of tasks to | ||
| #' \code{.Machine$integer.max}, so that progress is reported for | ||
| #' each element of X. | ||
| #' @returns List of core allocations. | ||
| #' | ||
| #' @export | ||
| #' @import data.table | ||
| #' @import BiocParallel | ||
| #' @importFrom parallel detectCores | ||
| set_cores <- function(workers = .90, | ||
| progressbar = TRUE, | ||
| verbose = TRUE) { | ||
|
|
||
| # Enable parallelization of HDF5 functions | ||
| ## Allocate ~10% of your available cores to non-parallelized processes | ||
| workers <- if (is.null(workers)) .90 else workers | ||
| total_cores <- parallel::detectCores() | ||
| if (workers < 1) { | ||
| reserved_cores <- ceiling(total_cores * (1 - workers)) | ||
| workers <- total_cores - reserved_cores | ||
| } else { | ||
| workers <- workers | ||
| reserved_cores <- total_cores - workers | ||
| } | ||
| messager(workers, "core(s) assigned as workers", | ||
| paste0("(",reserved_cores, " reserved)."), | ||
| v = verbose | ||
| ) | ||
| ### Ensure data.table doesn't interfere with parallelization #### | ||
| if(workers>1) data.table::setDTthreads(threads = 1) | ||
| #### Handle Windows #### | ||
| if (.Platform$OS.type == "windows") { | ||
| params <- BiocParallel::SnowParam(workers = workers, | ||
| progressbar = progressbar) | ||
| } else { | ||
| params <- BiocParallel::MulticoreParam(workers = workers, | ||
| progressbar = progressbar) | ||
| } | ||
| # DelayedArray::setAutoBPPARAM(params) | ||
| #### Not allowed to use internal functions #### | ||
| # DelayedArray:::set_verbose_block_processing(verbose) | ||
| return(params) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| #' Unlist a \link{data.table} | ||
| #' | ||
| #' \link{data.table}s can sometimes have columns that are nested lists. | ||
| #' This function will either drop these columns or convert them into | ||
| #' character strings. | ||
| #' @param dat \link{data.table} | ||
| #' @param drop Drop columns that are lists. | ||
| #' @param collapse Character to collapse lists with. | ||
| #' Used only when drop is \code{FALSE}. | ||
| #' @returns \link{data.table} | ||
| #' @export | ||
| #' @examples | ||
| #' dat <- data.table::data.table(a=1:3,b=list(1:2,3:4)) | ||
| #' unlist_dt(dat) | ||
| unlist_dt <- function(dat, | ||
| drop=FALSE, | ||
| collapse=";"){ | ||
| lst_cols <- sapply(dat, is.list) | ||
| if(isTRUE(drop)){ | ||
| messager("Dropping",length(lst_cols),"data.table columns.") | ||
| dat[,-c(lst_cols),with=FALSE] | ||
| } else{ | ||
| messager("Unlisting",length(lst_cols),"data.table columns.") | ||
| dat[,lapply(.SD, | ||
| function(x) if(is.list(x)) paste(unique(unlist(x)), | ||
| collapse = collapse) else x), | ||
| .SDcols = names(dat),by=.I] | ||
| } | ||
| } |
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