Update vignette

DESCRIPTION

@@ -12,6 +12,7 @@ Imports:
     AnVIL,
     BiocFileCache,
     dplyr,
+    GenomicRanges,
     httr,
     purrr,
     rtracklayer,

NAMESPACE

@@ -9,7 +9,6 @@ exportMethods(bb_example)
 exportMethods(bb_list_beds)
 exportMethods(bb_list_bedsets)
 exportMethods(bb_metadata)
-exportMethods(bb_metadata_files)
 exportMethods(bb_to_granges)
 exportMethods(bb_to_grangeslist)
 importFrom(AnVIL,Service)
@@ -19,6 +18,7 @@ importFrom(BiocFileCache,bfcdownload)
 importFrom(BiocFileCache,bfcneedsupdate)
 importFrom(BiocFileCache,bfcquery)
 importFrom(BiocFileCache,bfcrpath)
+importFrom(GenomicRanges,GRangesList)
 importFrom(R.utils,gunzip)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,filter)

R/bedbaser.R

@@ -267,31 +267,6 @@ setMethod(
     }
 )
 
-setGeneric(name = "bb_metadata_files",
-           def = function(x, id) { standardGeneric("bb_metadata_files") })
-
-#' BED files metadata
-#'
-#' @param id integer() BED record identifier
-#'
-#' @importFrom httr content
-#'
-#' @return tibble() file metadata
-#'
-#' @examples
-#' client <- BEDbase()
-#' ex_bed <- bb_example(client, "bed")
-#' mdf <- bb_metadata_files(client, ex_bed$id)
-#'
-#' @export
-setMethod(
-    "bb_metadata_files", "BEDbase",
-    function(x, id) {
-        md <- bb_metadata(x, id, "bed", TRUE)
-        .format_metadata_files(md$files)
-    }
-)
-
 setGeneric(name = "bb_to_granges",
            def = function(x, id, file_type = c("bed", "bigbed"),
                           extra_cols = NULL, quietly = FALSE) {
@@ -349,6 +324,8 @@ setGeneric(name = "bb_to_grangeslist",
 #' @param id integer() BEDset record identifier
 #' @param quietly logical() (defaults to FALSE) display messages
 #'
+#' @importFrom GenomicRanges GRangesList
+#'
 #' @return GRangesList() object
 #'
 #' @examples
@@ -360,7 +337,7 @@ setGeneric(name = "bb_to_grangeslist",
 setMethod(
     "bb_to_grangeslist", "BEDbase",
     function(x, id, quietly = FALSE) {
-        beds <- bb_beds_in_bedset(client, id)
+        beds <- bb_beds_in_bedset(x, id)
         gros <- list()
         for (id in beds$id) {
             gro <- bb_to_granges(x, id, "bed", quietly = quietly) 

R/utils.R

@@ -105,7 +105,7 @@
 #' @examples
 #' client <- BEDbase()
 #' ex_bed <- bb_example(client, "bed")
-#' md <- bb_metadata(client, ex_bed$id, "bed", TRUE).
+#' md <- bb_metadata(client, ex_bed$id, "bed", TRUE)
 #' file_path <- .get_file_path(md$files$bed_file$access_methods[[1]]$access_url$url,
 #'                             "bed")
 #' .bed_file_to_granges(file_path, bed_type, bed_format)

vignettes/bedbaser.Rmd

@@ -92,45 +92,59 @@ bb_beds_in_bedset(client, "excluderanges")
 
 ### Search for a BED file by keyword
 
-Search for BED files by keywords:
+Search for BED files by keywords. `bb_bed_text_search()` returns all BED files
+scored against a query.
 
 ```{r bb_search, eval=FALSE}
-# Currently not working correctly
-results <- bb_search(client, "hg13")
-results
+bb_bed_text_search(client, "hg13", limit = 10)
 ```
 
 ## Import a BED into a GRanges object
 
-`bb_to_granges` creates a GRanges object from a BED record identifier. It uses 
-`rtracklayer` to import the BED file. When column names are not known for BEDX+Y
-formats, a name is given indicating its position in the BED file.
+`bb_to_granges` downloads and imports a BED file into `rtracklayer` to
+create a GRanges object when given a BED record identifier.
 
-Note: Still in development, working for broadPeak, narrowPeak, and BEDX+0
+For BEDX+Y formats, a named list with column types may be passed through
+`extra_cols` if the column name and type are known. Otherwise, `bb_to_granges`
+attempts to guess the types and assigns column names. `bb_to_granges` assigns
+the proper name and types for broad peak and narrow peak files.
+
+`bb_to_granges` also attempts to pass the genome to `rtracklayer`
 
 ```{r bb_to_granges}
-rec_id1 <- "bbad85f21962bb8d972444f7f9a3a932"
-bed1 <- bb_metadata(client, rec_id1, rec_type = "bed")
-print(paste(bed1$name, "is in", bed1$bed_type, "format."))
-obj1 <- bb_to_granges(client, rec_id1, file_type="bed", quietly = TRUE)
-obj1
-
-# The following imports a BED4+1. Since we don't know the last column, we take
-# the column name and type from reading the table, which is V5.
-bed2 <- bb_metadata(client, example_bed$id, rec_type = "bed")
-print(paste(bed2$name, "is in", bed2$bed_type, "format."))
-obj2 <- bb_to_granges(client, example_bed$id, file_type="bed", quietly = TRUE)
-obj2
-# This is the same as
-# file_path <- "/home/meatbag/.cache/R/bedbaser/5611ae9d790f_04c46b96264ef40bca93f03b10345da5.bed"
-# import.bed(file_path, extraCols = c(V5 = numeric))
-```x`
+ex_bed <- bb_example(client, "bed")
+ex_bed$bed_type
+ex_bed$genome_alias
+bb_to_granges(client, ex_bed$id, "bed")
+
+ex_bed <- bb_example(client, "bed")
+ex_bed$bed_type
+bb_to_granges(client, ex_bed$id, "bed", extra_cols = c("testing" = "character"))
+
+id <- "bbad85f21962bb8d972444f7f9a3a932"
+md <- bb_metadata(client, id, "bed", TRUE)
+md$bed_format
+md$bed_type
+bb_to_granges(client, id, "bed")
+```
+
+`bb_to_granges` can also import big BED files.
+
+```{r bb_to_granges_big_bed}
+ex_bed <- bb_example(client, "bed")
+bb_to_granges(client, ex_bed$id, "bigbed")
+```
+# Import a BEDset into a GRangesList
+
+`bb_to_grangeslist` creates GRangesList object given a BEDset record identifier.
+
+```{r bb_to_grangeslist}
+id <- "lola_hg38_ucsc_features"
+bb_to_grangeslist(client, id)
+```
 
 ## SessionInfo()
 
 ```{r sessionInfo}
 sessionInfo()
-```   
-Notes: For metadata in R, maybe create a tibble from some reasonable level of untested data, then demo use of tidy::unnest_wider() / unnest_longer(),  GRanges as plyranges?
-
-Can you specify the column names interactively? 
+```