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Fix grammar, remove cache structure example
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jwokaty committed Jan 29, 2025
1 parent da57b26 commit 466392b
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2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,6 +1,6 @@
Package: bedbaser
Title: A BEDbase client
Version: 0.99.22
Version: 0.99.23
Authors@R: c(
person(
given = "Andres",
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45 changes: 18 additions & 27 deletions R/bedbaser.R
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Expand Up @@ -21,14 +21,8 @@
#' GRangesList.
#'
#' @details \code{BEDbase()} creates a cache similar to that of the
#' [Geniml BBClient's cache](https://docs.bedbase.org/geniml):
#' \code{
#' cache_path
#' bedfiles
#' a/f/afile.bed.gz
#' bedsets
#' a/s/aset.txt
#' }
#' [Geniml BBClient's cache](https://docs.bedbase.org/geniml).
#'
#' The convenience functions are as follows
#' * `bedbaser::BEDbase()`: API service constructor
#' * `bedbaser::getCache()`: Retrieve cache
Expand Down Expand Up @@ -135,12 +129,7 @@ setGeneric(
#' Set cache along path
#'
#' @description Create a cache for BED files and BEDsets like
#' [Geniml BBClient's cache](https://docs.bedbase.org/geniml):
#' cache_path
#' bedfiles
#' a/f/afile.bed.gz
#' bedsets
#' a/s/aset.txt
#' [Geniml BBClient's cache](https://docs.bedbase.org/geniml).
#'
#' @param x BEDbase() object
#' @param cache_path character(1)
Expand Down Expand Up @@ -171,8 +160,8 @@ setMethod(

#' Display API functions
#'
#' @description Display functions defined through the bedhost API and their
#' corresponding parameters.
#' @description Display functions defined through the
#' [bedhost API](https://api.bedbase.org) and their corresponding parameters.
#'
#' @param x BEDbase() object
#' @param ... other options
Expand Down Expand Up @@ -217,7 +206,7 @@ setMethod(
#' Display functions for a tag
#'
#' @description Display functions available through the API associated with a
#' tag keyword in bedhost.
#' tag keyword in [bedhost](https://api.bedbase.org).
#'
#' @param x BEDbase() object
#' @param .tags character() tags for filtering operations
Expand All @@ -242,9 +231,9 @@ setMethod(

#' Get the example BED file or BEDset with metadata
#'
#' @description Get the example BED file or BEDset available through bedhost.
#' Useful for an initial exploration of bedbaser with an example BED file and
#' BEDset in BEDbase.
#' @description Get the example BED file or BEDset available through
#' [bedhost](https://api.bedbase.org). Useful for an initial exploration
#' of bedbaser with an example BED file and BEDset in BEDbase.
#'
#' @param bedbase BEDbase() object
#' @param rec_type character(1) bed or bedset
Expand Down Expand Up @@ -315,8 +304,9 @@ bb_metadata <- function(bedbase, id, full = FALSE) {

#' List BEDs
#'
#' @description List BED files available through bedhost. By default uses the
#' bedhost default of 1000 records and an initial offset of 0.
#' @description List BED files available through
#' [bedhost](https://api.bedbase.org). By default uses the bedhost default
#' of 1000 records and an initial offset of 0.
#'
#' @rdname bb_list_beds
#'
Expand Down Expand Up @@ -355,8 +345,9 @@ bb_list_beds <- function(

#' List BEDsets
#'
#' @description List BEDsets available through bedhost. By default uses the
#' bedhost default of 1000 records and an initial offset of 0.
#' @description List BEDsets available through
#' [bedhost](https://api.bedbase.org). By default uses the bedhost default
#' of 1000 records and an initial offset of 0.
#'
#' @rdname bb_list_bedsets
#'
Expand Down Expand Up @@ -423,9 +414,9 @@ bb_beds_in_bedset <- function(bedbase, bedset_id) {

#' Search BED files by text
#'
#' @description Return all available BED file ranked by relevance to the
#' keywords. Uses the bedhost default of 10 records and an initial
#' offset of 0.
#' @description Return all available BED files ranked by relevance to the
#' keywords. Uses the [bedhost API](https://api.bedbase.org) default of 10
#' records and an initial offset of 0.
#'
#' @rdname bb_bed_text_search
#'
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10 changes: 2 additions & 8 deletions man/BEDbase.Rd

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6 changes: 3 additions & 3 deletions man/bb_bed_text_search.Rd

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6 changes: 3 additions & 3 deletions man/bb_example.Rd

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5 changes: 3 additions & 2 deletions man/bb_list_beds.Rd

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5 changes: 3 additions & 2 deletions man/bb_list_bedsets.Rd

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4 changes: 2 additions & 2 deletions man/operations-BEDbase-method.Rd

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7 changes: 1 addition & 6 deletions man/setCache-BEDbase-method.Rd

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2 changes: 1 addition & 1 deletion man/tags-BEDbase-method.Rd

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