debugging features

NAMESPACE

@@ -26,7 +26,6 @@ export(sv_to_bedpe_file)
 export(sv_to_custom_track)
 export(tidy_lymphgen)
 export(view_mutation_igv)
-import(GAMBLR.data)
 import(GAMBLR.helpers)
 import(GenomicRanges, except = c("start", "end", "merge", "shift", "union", "intersect", "setdiff", "reduce", "trim"))
 import(S4Vectors, except = c("merge", "second", "first", "union", "intersect", "setdiff", "setequal", "rename", "expand", "head", "tail", "end", "start"))

R/build_browser_hub.R

@@ -71,7 +71,7 @@
 #'
 #' @return Nothing.
 #' 
-#' @import dplyr GAMBLR.helpers
+#' @import dplyr
 #' @export
 #'
 #' @examples
@@ -113,7 +113,8 @@ build_browser_hub = function(maf_data,
                              contact_email,
                              visibility = "squish",
                              bigDataUrl_base = "https://github.com/morinlab/LLMPP/blob/main",
-                             bedToBigBed_path){
+                             bedToBigBed_path,
+                             verbose=FALSE){
 
   # check some provided parameter 
   stopifnot("`these_seq_types` must be one or more of \"genome\" or \"capture\"." = 
@@ -134,6 +135,10 @@ build_browser_hub = function(maf_data,
       }
     )
   }else{
+    if(dir.exists(bedToBigBed_path)){
+      #directory was provided, add expected binary name
+      bedToBigBed_path = paste0(bedToBigBed_path,"/bedToBigBed")
+    }
     stopifnot("`bedToBigBed_path` points to a non-existent file." = 
                 file.exists(bedToBigBed_path))
   }
@@ -147,7 +152,10 @@ build_browser_hub = function(maf_data,
             this_seq_type = these_seq_types_i)
   }) %>% 
     suppressMessages
-
+  if(verbose){
+    group_by(these_samples_metadata$genome,seq_type,pathology) %>% tally() %>% print()
+    group_by(these_samples_metadata$capture,seq_type,pathology) %>% tally() %>% print()
+  }
   # check provided splitColumnName parameter 
   stopifnot("`splitColumnName` must be a column name contained in the metadata." = 
               splitColumnName %in% names(these_samples_metadata[[1]]))
@@ -188,6 +196,9 @@ build_browser_hub = function(maf_data,
   regions_bed = dplyr::select(regions_bed, 1,2,3) %>% 
     arrange( .[[1]], .[[2]] )
   temp_bed = tempfile(pattern = "regionsBed_", fileext = ".bed")
+  if(verbose){
+    print(paste("writing temporary file:",temp_bed))
+  }
   write.table(regions_bed, temp_bed, quote = FALSE, sep = "\t", row.names = FALSE, 
               col.names = FALSE)
   if(projection == "grch37"){
@@ -213,13 +224,22 @@ build_browser_hub = function(maf_data,
   # get maf data from the specified regions and metadata/samples (for each seq type)
   if(missing(maf_data)){
     maf_data = mapply(function(these_seq_types_i, these_samples_metadata_i){
-      get_ssm_by_regions(regions_bed = regions_bed,
+      if(verbose){
+        get_ssm_by_regions(regions_bed = regions_bed,
+                           this_seq_type = these_seq_types_i,
+                           these_samples_metadata = these_samples_metadata_i, 
+                           projection = projection,
+                           streamlined = FALSE, 
+                           basic_columns = TRUE) 
+      }else{
+        get_ssm_by_regions(regions_bed = regions_bed,
                          this_seq_type = these_seq_types_i,
                          these_samples_metadata = these_samples_metadata_i, 
                          projection = projection,
                          streamlined = FALSE, 
                          basic_columns = TRUE) %>% 
-        suppressMessages
+          suppressMessages
+      }
     }, these_seq_types, these_samples_metadata, SIMPLIFY = FALSE)
   }else{
     maf_data = mapply(function(these_seq_types_i, these_samples_metadata_i){

R/gene_to_region.R

@@ -29,7 +29,8 @@ gene_to_region = function(gene_symbol,
                           ensembl_id,
                           projection = "grch37",
                           return_as = "region",
-                          sort_regions = TRUE){
+                          sort_regions = TRUE,
+                          pad_length = 0){
 
   stopifnot('`projection` parameter must be "grch37" or "hg38"' = projection %in% c("grch37", "hg38"))
   stopifnot('`return_as` parameter must be "region", "bed" or "df"' = return_as %in% c("region", "bed", "df"))
@@ -64,7 +65,7 @@ gene_to_region = function(gene_symbol,
   region = dplyr::select(gene_coordinates, chromosome, start, end, gene_name, hugo_symbol, ensembl_gene_id) %>%
     as.data.frame() %>% 
     dplyr::filter(chromosome %in% chr_select)
-
+  region = mutate(region, start = start - pad_length, end = end + pad_length)
   if(sort_regions){
     if(projection == "grch37"){
       chrm_num = region$chromosome

R/liftover.R

@@ -25,7 +25,7 @@
 #' @rawNamespace import(S4Vectors, except = c("merge", "second", "first", "union", "intersect", "setdiff", "setequal", "rename", "expand", "head", "tail", "end", "start"))
 #' @rawNamespace import(GenomicRanges, except = c("start", "end", "merge", "shift", "union", "intersect", "setdiff", "reduce", "trim"))
 #' @rawNamespace import(rtracklayer, except = c("start", "end"))
-#' @import dplyr tidyr readr GAMBLR.data
+#' @import dplyr tidyr readr
 #' @export
 #'
 #' @examples