Search BED files by text

Return all available BED files ranked by relevance to the keywords. Uses the bedhost API default of 10 records and an initial offset of 0.

bb_bed_text_search(
  bedbase,
  query,
  genome = NULL,
  assay = NULL,
  limit = 10,
  offset = 0
)

Arguments

bedbase

BEDbase() object

query

character() keywords to search

genome

character() (default NULL) genome to search

assay

character() (default NULL) assay to search

limit

integer(1) (default 10) maximum number of results

offset

integer(1) (default 0) page offset of results

Value

tibble of results

Examples

bedbase <- BEDbase()
#> 130451 BED files available.
bb_bed_text_search(bedbase, "hg38")
#> # A tibble: 10 × 46
#>    id              payload.id payload.name payload.description payload.cell_line
#>    <chr>           <chr>      <chr>        <chr>               <chr>            
#>  1 2d86ffa3f593c7… 2d86ffa3f… hg38.Reddy.… "Defined by the EN… ""               
#>  2 6be4f1fb7464a8… 6be4f1fb7… ChIP_HL60_H… ""                  "HL-60"          
#>  3 3d80a48ef0b4a4… 3d80a48ef… hg38.UCSC.h… "Gaps from large b… ""               
#>  4 3986a74ae4f050… 3986a74ae… ChIP_HL60_H… ""                  "HL-60"          
#>  5 5691d9009f9614… 5691d9009… ChIP_HL60_H… ""                  "HL-60"          
#>  6 388b4b726e760a… 388b4b726… hg38.Lareau… "ENCODE excludable… ""               
#>  7 2b93bec4ddad5f… 2b93bec4d… hg38.Nordin… "Defined from CUT&… ""               
#>  8 1b7fc14e60f8af… 1b7fc14e6… ChIP_HL60_H… ""                  "HL-60"          
#>  9 1f78a65cddf6a1… 1f78a65cd… hg38.Kundaj… "Defined by Anshul… ""               
#> 10 9f17013256fca6… 9f1701325… HT1376_DMSO… ""                  "HT1376"         
#> # ℹ 41 more variables: payload.cell_type <chr>, payload.tissue <chr>,
#> #   payload.target <chr>, payload.treatment <chr>, payload.assay <chr>,
#> #   payload.genome_alias <chr>, payload.genome_digest <chr>,
#> #   payload.species_name <chr>, score <chr>, metadata.name <chr>,
#> #   metadata.genome_alias <chr>, metadata.genome_digest <chr>,
#> #   metadata.bed_compliance <chr>, metadata.data_format <chr>,
#> #   metadata.compliant_columns <chr>, metadata.non_compliant_columns <chr>, …