vignettes/bedbaser.Rmd
+ Source: vignettes/bedbaser.Rmd
bedbaser.RmdSet the cache path with the argument cache_path;
-otherwise, bedbaser will choose the default cache location.
Set the cache path with the argument cache_path. If
+cache_path is not set, bedbaser will choose the default
+location. bedbaser can use the same cache as bbclient
+available through the genomic interval machine learning toolkit
+geniml by setting the cache_path to the same
+location.
+bb_list_beds(api)-## # A tibble: 1,000 × 26 ## name genome_alias genome_digest bed_type bed_format id description @@ -146,7 +154,7 @@Find a BED file or BEDset## # annotation.phenotype <chr>, annotation.description <chr>, ## # annotation.cell_type <chr>, annotation.cell_line <chr>, ## # annotation.tissue <chr>, annotation.library_source <chr>, …
+bb_list_bedsets(api)## # A tibble: 19,864 × 9 ## id name md5sum submission_date last_update_date description bed_ids @@ -169,7 +177,7 @@Examine metadata
Use
-bb_metadata()to learn more about a BED or BEDset associated with an id.+@@ -196,7 +204,7 @@ex_bed <- bb_example(api, "bed") md <- bb_metadata(api, ex_bed$id) head(md)Show BED files in BEDset
Use
-bb_beds_in_bedset()to display the id of BEDs in a BEDset.+bb_beds_in_bedset(api, "excluderanges")## # A tibble: 81 × 26 ## name genome_alias genome_digest bed_type bed_format id description @@ -224,7 +232,7 @@Search for a BED file by keyword
Search for BED files by keywords.
-bb_bed_text_search()returns all BED files scored against a keyword query.+bb_bed_text_search(api, "cancer", limit = 10)## # A tibble: 10 × 43 ## id payload.species_name payload.species_id payload.genotype @@ -253,7 +261,7 @@Import a BED into a GRanges objectCreate a GRanges object with a BED id with
bb_to_granges, which downloads and imports a BED file using rtracklayer. -+ex_bed <- bb_example(api, "bed") head(ex_bed)-## $name @@ -273,7 +281,7 @@Import a BED into a GRanges object## ## $id ## [1] "233479aab145cffe46221475d5af5fae"
+# Allow bedbaser to assign column names and types bb_to_granges(api, ex_bed$id, quietly = FALSE)## GRanges object with 51701 ranges and 0 metadata columns: @@ -296,12 +304,12 @@if the column name and type are known. Otherwise,Import a BED into a GRanges objectextra_cols
bb_to_grangesguesses the column types and assigns column names. -+# Manually assign column name and type using `extra_cols` bb_to_granges(api, ex_bed$id, extra_cols = c("column_name" = "character"))-
bb_to_grangesautomatically assigns the column names and types for broad peak and narrow peak files.+-@@ -322,7 +330,7 @@bed_id <- "bbad85f21962bb8d972444f7f9a3a932" md <- bb_metadata(api, bed_id) head(md)Import a BED into a GRanges object## ## $id ## [1] "bbad85f21962bb8d972444f7f9a3a932"
+bb_to_granges(api, bed_id)## GRanges object with 26210 ranges and 6 metadata columns: ## seqnames ranges strand | name score @@ -354,7 +362,7 @@Import a BED into a GRanges object## ------- ## seqinfo: 711 sequences (1 circular) from hg38 genome
-
bb_to_grangescan also import big BED files.+bed_id <- "ffc1e5ac45d923135500bdd825177356" bb_to_granges(api, bed_id, "bigbed", quietly = FALSE)@@ -393,7 +401,7 @@## Error passing genome. Attempting to create GRanges object without genome.Import a BEDset into a GRangesList
Create a GRangesList given a BEDset id with
-bb_to_grangeslist.+bedset_id <- "lola_hg38_ucsc_features" bb_to_grangeslist(api, bedset_id)## GRangesList object of length 11: @@ -424,7 +432,7 @@Accessing BEDbase API endpoints
Because bedbaser uses the AnVIL Service class, it’s possible to access any endpoint of the BEDbase API.
-+show(api)## service: bedbase ## tags(); use bedbase$<tab completion>: @@ -452,14 +460,14 @@and use httr to get the result.Accessing BEDbase API endpoints$
showwill display information about the endpoint. -+## ## Attaching package: 'httr'-## The following object is masked from 'package:Biobase': ## ## content+show(api$get_bed_stats_v1_bed__bed_id__metadata_stats_get)-## get_bed_stats_v1_bed__bed_id__metadata_stats_get ## Get stats for a single BED record @@ -469,7 +477,7 @@Accessing BEDbase API endpoints## Parameters: ## bed_id (string) ## BED digest
+@@ -535,7 +543,7 @@id <- "bbad85f21962bb8d972444f7f9a3a932" rsp <- api$get_bed_stats_v1_bed__bed_id__metadata_stats_get(id) content(rsp)Example: Change
Install liftOver and rtracklayer then load the packages.
-+if (!"BiocManager" %in% rownames(installed.packages())) { install.packages("BiocManager") } @@ -546,7 +554,7 @@Example: Change
Create a GRanges object from a mouse genome. Create a BEDbase Service instance. Use the instance to create a GRanges object from the BEDbase
-id.+id <- "7816f807ffe1022f438e1f5b094acf1a" api <- BEDbase() gro <- bb_to_granges(api, id) @@ -582,7 +590,7 @@Example: Change ## seqinfo: 239 sequences (1 circular) from mm10 genome
Download the chain file from UCSC.
-@@ -32,7 +32,7 @@ Changelog+chain_url <- paste0( "https://hgdownload.cse.ucsc.edu/goldenPath/mm10/liftOver/", "mm10ToMm39.over.chain.gz" @@ -593,7 +601,7 @@Example: Change gunzip(gz, remove = FALSE)
Import the chain, set the sequence levels style, and set the genome for the GRanges object.
-diff --git a/news/index.html b/news/index.html index fdc4aae..a08c795 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13+@@ -51,7 +51,7 @@ch <- import.chain(file.path(tmpdir, "mm10ToMm39.over.chain")) seqlevelsStyle(gro) <- "UCSC" gro39 <- liftOver(gro, ch) @@ -633,7 +641,7 @@Example: Change
@@ -32,7 +32,7 @@ ChangelogSessionInfo()
-@@ -32,7 +32,7 @@ Changelog+## R Under development (unstable) (2024-11-27 r87386) ## Platform: x86_64-pc-linux-gnu @@ -660,7 +668,7 @@SessionInfo()## ## other attached packages: ## [1] httr_1.4.7 -## [2] bedbaser_0.99.12 +## [2] bedbaser_0.99.13 ## [3] liftOver_1.30.0 ## [4] Homo.sapiens_1.3.1 ## [5] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 @@ -702,13 +710,13 @@
SessionInfo()## [31] R6_2.5.1 fastmap_1.2.0 ## [33] shiny_1.9.1 GenomeInfoDbData_1.2.13 ## [35] MatrixGenerics_1.19.0 digest_0.6.37 -## [37] textshaping_0.4.0 RSQLite_2.3.8 +## [37] textshaping_0.4.0 RSQLite_2.3.9 ## [39] filelock_1.0.3 fansi_1.0.6 ## [41] abind_1.4-8 compiler_4.5.0 ## [43] withr_3.0.2 bit64_4.5.2 ## [45] BiocParallel_1.41.0 DBI_1.2.3 ## [47] biomaRt_2.63.0 rappdirs_0.3.3 -## [49] DelayedArray_0.33.2 rjson_0.2.23 +## [49] DelayedArray_0.33.3 rjson_0.2.23 ## [51] tools_4.5.0 httpuv_1.6.15 ## [53] glue_1.8.0 restfulr_0.0.15 ## [55] promises_1.3.2 grid_4.5.0 diff --git a/articles/index.html b/articles/index.html index faadf5b..39a7274 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13
- - + @@ -63,20 +63,20 @@
Authors and Citation
Wokaty J, Waldron L (2024). bedbaser: A BEDbase client. -R package version 0.99.12, https://github.com/waldronlab/bedbaser. +R package version 0.99.13, https://github.com/waldronlab/bedbaser.
@Manual{, title = {bedbaser: A BEDbase client}, author = {Jen Wokaty and Levi Waldron}, year = {2024}, - note = {R package version 0.99.12}, + note = {R package version 0.99.13}, url = {https://github.com/waldronlab/bedbaser}, }diff --git a/index.html b/index.html index 76e0d28..56aeb36 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ bedbaser - 0.99.12 + 0.99.13
- - + @@ -47,7 +47,7 @@
diff --git a/pkgdown.yml b/pkgdown.yml index 05ddb1d..18918ca 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,4 +3,4 @@ pkgdown: 2.1.1.9000 pkgdown_sha: dfa28bef27858bd442334b5cce8f645d555914be articles: bedbaser: bedbaser.html -last_built: 2024-12-03T17:26Z +last_built: 2024-12-04T21:37Z diff --git a/reference/BEDbase-class.html b/reference/BEDbase-class.html index 270dda0..7e31a7a 100644 --- a/reference/BEDbase-class.html +++ b/reference/BEDbase-class.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13@@ -32,7 +32,7 @@ Changelog
- - + @@ -47,7 +47,7 @@
diff --git a/reference/BEDbase.html b/reference/BEDbase.html index 309760b..1ea80e5 100644 --- a/reference/BEDbase.html +++ b/reference/BEDbase.html @@ -19,7 +19,7 @@ bedbaser - 0.99.12 + 0.99.13@@ -34,7 +34,7 @@ Changelog
- - + @@ -49,7 +49,7 @@
@@ -89,7 +89,9 @@Value
@@ -32,7 +32,7 @@ ChangelogDetails
-The convenience functions are as follows
- +
bedbaser::BEDbase(): API service constructorbedbaser can use the same cache as the geniml bbclient. Set the +cache_path to the geniml cache when creating the instance.
+The convenience functions are as follows
bedbaser::BEDbase(): API service constructor
bedbaser::getCache(): Retrieve cache
bedbaser::setCache(): Set path to cache- diff --git a/reference/bb_bed_text_search.html b/reference/bb_bed_text_search.html index b8ee6d3..a00719c 100644 --- a/reference/bb_bed_text_search.html +++ b/reference/bb_bed_text_search.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13
bedbaser::bb_example(): Retrieve an example BED file or BEDset
- - + @@ -47,7 +47,7 @@
diff --git a/reference/bb_beds_in_bedset.html b/reference/bb_beds_in_bedset.html index 9724d3f..60d2c87 100644 --- a/reference/bb_beds_in_bedset.html +++ b/reference/bb_beds_in_bedset.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13@@ -32,7 +32,7 @@ Changelog
- - + @@ -47,7 +47,7 @@
diff --git a/reference/bb_example.html b/reference/bb_example.html index 77e9acf..c48e108 100644 --- a/reference/bb_example.html +++ b/reference/bb_example.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13@@ -32,7 +32,7 @@ Changelog
- - + @@ -47,7 +47,7 @@
@@ -32,7 +32,7 @@ Changelogdiff --git a/reference/bb_list_beds.html b/reference/bb_list_beds.html index aaa050d..b69d18c 100644 --- a/reference/bb_list_beds.html +++ b/reference/bb_list_beds.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13Get the example BED file or BEDset with metadata
- Source:R/bedbaser.R+ Source:R/bedbaser.Rbb_example.Rd
- - + @@ -47,7 +47,7 @@
diff --git a/reference/bb_list_bedsets.html b/reference/bb_list_bedsets.html index fce8210..b2410d5 100644 --- a/reference/bb_list_bedsets.html +++ b/reference/bb_list_bedsets.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13@@ -32,7 +32,7 @@ Changelog
- - + @@ -47,7 +47,7 @@
diff --git a/reference/bb_metadata.html b/reference/bb_metadata.html index 9c3b4ab..998eff7 100644 --- a/reference/bb_metadata.html +++ b/reference/bb_metadata.html @@ -18,7 +18,7 @@ bedbaser - 0.99.12 + 0.99.13@@ -33,7 +33,7 @@ Changelog
- - + @@ -48,7 +48,7 @@
diff --git a/reference/bb_save.html b/reference/bb_save.html index f00366d..b578c66 100644 --- a/reference/bb_save.html +++ b/reference/bb_save.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13@@ -32,7 +32,7 @@ Changelog
- - + @@ -47,7 +47,7 @@
@@ -32,7 +32,7 @@ Changelogdiff --git a/reference/bb_to_granges.html b/reference/bb_to_granges.html index dfce1e1..a37767d 100644 --- a/reference/bb_to_granges.html +++ b/reference/bb_to_granges.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13Save a BED or BEDset files to a path given an id
- Source:R/bedbaser.R+ Source:R/bedbaser.Rbb_save.Rd
- - + @@ -47,7 +47,7 @@
@@ -32,7 +32,7 @@ Changelogdiff --git a/reference/bb_to_grangeslist.html b/reference/bb_to_grangeslist.html index 5333da5..73d56c7 100644 --- a/reference/bb_to_grangeslist.html +++ b/reference/bb_to_grangeslist.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13Create a GRanges object given a BED id
- Source:R/bedbaser.R+ Source:R/bedbaser.Rbb_to_granges.Rd
- - + @@ -47,7 +47,7 @@
@@ -32,7 +32,7 @@ Changelogdiff --git a/reference/bedbaser-package.html b/reference/bedbaser-package.html index 432eae0..5e256a6 100644 --- a/reference/bedbaser-package.html +++ b/reference/bedbaser-package.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13Create a GRangesList object given a BEDset id
- Source:R/bedbaser.R+ Source:R/bedbaser.Rbb_to_grangeslist.Rd
- - + @@ -47,7 +47,7 @@
@@ -32,7 +32,7 @@ Changelog@@ -59,7 +59,7 @@bedbaser: A BEDbase client
- Source:R/bedbaser-package.R+ Source:R/bedbaser-package.Rbedbaser-package.Rdbedbaser: A BEDbase client
See also
Useful links:
- -
- +
Report bugs at https://github.com/jwokaty/bedbaser/issues
Report bugs at https://github.com/waldronlab/bedbaser/issues
diff --git a/reference/getCache-BEDbase-method.html b/reference/getCache-BEDbase-method.html index bc764c1..ce8ae27 100644 --- a/reference/getCache-BEDbase-method.html +++ b/reference/getCache-BEDbase-method.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13@@ -32,7 +32,7 @@ Changelog
- - + @@ -47,7 +47,7 @@
@@ -83,7 +83,7 @@@@ -32,7 +32,7 @@ ChangelogExamples
#> 19974 BED files available. getCache(api) #> class: BiocFileCache -#> bfccache: /tmp/RtmpFZB8Vq +#> bfccache: /tmp/RtmpqV4vho #> bfccount: 0 #> For more information see: bfcinfo() or bfcquery() diff --git a/reference/index.html b/reference/index.html index ab19e50..43af60a 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13
- - + @@ -47,7 +47,7 @@
diff --git a/reference/setCache-BEDbase-method.html b/reference/setCache-BEDbase-method.html index c7b056e..e4854e5 100644 --- a/reference/setCache-BEDbase-method.html +++ b/reference/setCache-BEDbase-method.html @@ -17,7 +17,7 @@ bedbaser - 0.99.12 + 0.99.13@@ -32,7 +32,7 @@ Changelog
- - + @@ -47,7 +47,7 @@
@@ -80,6 +80,10 @@+Arguments
Value
BiocFileCache cache of BED files
+Details
+bedbaser can use the same cache as bbclient
+Examples