Handling of bundled data through designated separate repo

DESCRIPTION

@@ -29,6 +29,7 @@ Imports:
     dplyr,
     forcats,
     g3viz,
+    GAMBLR.data (>= 0.1),
     ggbeeswarm,
     ggplot2,
     ggpubr,
@@ -68,7 +69,8 @@ VignetteBuilder:
 Remotes:
     cBioPortal/cgdsr,
     morinlab/g3viz,
-    morinlab/ggsci
+    morinlab/ggsci,
+    morinlab/GAMBLR.data
 biocViews:
 Encoding: UTF-8
 LazyData: true

NAMESPACE

@@ -106,6 +106,7 @@ export(tidy_lymphgen)
 export(write_sample_set_hash)
 import(ComplexHeatmap)
 import(DBI)
+import(GAMBLR.data)
 import(RCircos)
 import(RColorBrewer)
 import(RMariaDB)

R/data.R

@@ -235,24 +235,6 @@
 "grch37_all_gene_coordinates"
 
 
-#' grch37 ASHM Regions.
-#'
-#' ASHM regions in respect to grch37.
-#'
-#' @format ## `grch37_ashm_regions`
-#' A data frame with 88 rows and 7 columns.
-#' \describe{
-#'   \item{chr_name}{The chromosome for which the region is residing on}
-#'   \item{hg19_start}{start coordinate for the region}
-#'   \item{hg19_end}{end coordinate for the region}
-#'   \item{gene}{Gene symbol (Hugo)}
-#'   \item{region}{Region name}
-#'   \item{regulatory_comment}{Regulatory element}
-#'   \item{name}{gene-region format}
-#' }
-"grch37_ashm_regions"
-
-
 #' grch37 Gene Coordinates.
 #'
 #' All gene coordinates in respect to grch37.
@@ -300,25 +282,6 @@
 #' }
 "grch37_partners"
 
-
-#' hg38 ASHM Regions.
-#'
-#' ASHM regions in respect to hg38.
-#'
-#' @format ## `hg38_ashm_regions`
-#' A data frame with 88 rows and 7 columns.
-#' \describe{
-#'   \item{chr_name}{The chromosome for which the region is residing on}
-#'   \item{hg19_start}{start coordinate for the region}
-#'   \item{hg19_end}{end coordinate for the region}
-#'   \item{gene}{Gene symbol (Hugo)}
-#'   \item{region}{Region name}
-#'   \item{regulatory_comment}{Regulatory element}
-#'   \item{name}{gene-region format}
-#' }
-"hg38_ashm_regions"
-
-
 #' hg38 Gene Coordinates.
 #'
 #' All gene coordinates in respect to hg38.
@@ -415,29 +378,6 @@
 "lymphoma_genes_comprehensive"
 
 
-#' Lymphoma Genes
-#'
-#' A data frame with known lymphoma genes, genes are annotated by pathology, as well as literature support.
-#'
-#' @format ## `lymphoma_genes`
-#' A data frame with 196 rows and 12 columns.
-#' \describe{
-#'   \item{Gene}{Gene symbol}
-#'   \item{DLBCL}{Boolean flag annotating if the described genes are significant for the pathology (DLBCL)}
-#'   \item{FL}{Boolean flag annotating if the described genes are significant for the pathology (FL)}
-#'   \item{BL}{Boolean flag annotating if the described genes are significant for the pathology (BL)}
-#'   \item{MCL}{Boolean flag annotating if the described genes are significant for the pathology (MCL)}
-#'   \item{CLL}{Boolean flag annotating if the described genes are significant for the pathology (CLL)}
-#'   \item{ensembl_gene_id}{Ensembl gene ID}
-#'   \item{hgnc_symbol}{Gene symbol (Hugo)}
-#'   \item{LymphGen}{Boolean flag, TRUE if lymphGen}
-#'   \item{Reddy}{Boolean flag, TRUE if gene verified by the stated study (Reddy)}
-#'   \item{Chapuy}{Boolean flag, TRUE if gene verified by the stated study (Chapuy)}
-#'   \item{entrezgene_id}{Entrez ID for the described gene}
-#' }
-"lymphoma_genes"
-
-
 #' Reddy Genes.
 #'
 #' Genes identified as significantly mutated in DLBCL by the study of Reddy et al.

R/load_data.R

@@ -0,0 +1,108 @@
+# Helper functions not for export
+
+#' @title Check the version of the data to load.
+#'
+#' @description Helper function to determine whether the user is requesting the latest version
+#' of the bundled data or wants to access one of the earlier veresions.
+#'
+#' @param mode Determines which data to handle. Defaults to somatic_hypermutation_locations. Will grow with more options as more data is version tracked.
+#' @param this_genome_build The genome build of the data if coordinate-based. Accepts grch37 (default) or hg38.
+#'
+#' @noRd
+#'
+#' @return data frame
+#' @import config dplyr readr GAMBLR.data
+#'
+#' @examples
+#' determine_version()
+#' determine_version(this_genome_build = "hg38")
+#'
+determine_version <- function(
+    mode = "somatic_hypermutation_locations",
+    this_genome_build = "grch37"
+){
+    # Determine the latest version of the data
+    # Get absolute paths to bundled files in GAMBLR.data
+    all_files <- system.file(
+        "extdata",
+        package = "GAMBLR.data"
+    ) %>%
+    list.files(
+        recursive = TRUE,
+        full.names = TRUE
+    )
+
+    # Extract version from the path
+    all_files <- gsub(
+        ".*extdata/",
+        "",
+        all_files
+    )
+    all_files <- all_files[grepl(mode, all_files)]
+
+    # Determine the highst version
+    versions <- gsub(".*[/]([^/]+)[/].*", "\\1", all_files)
+    versions <- versions[grep('[0-9]+', versions)]
+    versions <- sort(
+        numeric_version(
+            versions
+            )
+    )
+
+    latest_version <- max(versions)
+
+    # Which version did the user requested in config?
+    requested_version <- check_config_value(
+        config::get("bundled_data_versions")[[mode]]
+    )
+    # Convert to numeric value if it is a string
+    if(requested_version == "_latest"){
+        requested_version = latest_version
+    }
+
+    # UCSC-ize the genome build format of GAMBLR
+    if(this_genome_build == "grch37"){
+        this_genome_build = "GRCh37"
+    }else{
+        this_genome_build = "GRCh38"
+    }
+
+    # Load the user-specified version of the data
+    this_object <- paste0(
+        mode,
+        "_",
+        this_genome_build,
+        "_v",
+        requested_version
+    )
+
+    this_data <- eval(
+        parse(
+            text = paste0(
+                "GAMBLR.data::",
+                this_object)
+            )
+    )
+
+    return(this_data)
+
+}
+
+
+grch37_ashm_regions <- determine_version(
+    mode = "somatic_hypermutation_locations",
+    this_genome_build = "grch37"
+)
+
+hg38_ashm_regions <- determine_version(
+    mode = "somatic_hypermutation_locations",
+    this_genome_build = "hg38"
+)
+
+lymphoma_genes <- GAMBLR.data::get_genes(
+    entities = c("BL", "MCL", "DLBCL"),
+    version = check_config_value(
+        config::get("bundled_data_versions")[["lymphoma_genes"]]
+    ),
+    gene_format = "data.frame"
+)