hide function for checking ids

waldronlab · Mar 22, 2024 · 51e9717 · 51e9717
1 parent 5ca6d1b
commit 51e9717
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Showing 5 changed files with 3 additions and 52 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: bugphyzz
 Title: A harmonized data resource and software for enrichment analysis of microbial physiologies
-Version: 0.0.1.8
+Version: 0.0.1.9
 Authors@R: 
     c(
         person(

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(check_valid_ncbi_ids)
 export(getTaxonSignatures)
 export(importBugphyzz)
 export(makeSignatures)
@@ -12,24 +11,17 @@ importFrom(crayon,red)
 importFrom(dplyr,across)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,group_by)
-importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
-importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
-importFrom(magrittr,"%>%")
 importFrom(magrittr,set_colnames)
 importFrom(methods,as)
 importFrom(purrr,discard)
 importFrom(purrr,map)
 importFrom(purrr,map2)
 importFrom(purrr,modify_depth)
 importFrom(purrr,set_names)
-importFrom(taxize,classification)
-importFrom(taxizedb,taxid2name)
-importFrom(tibble,as_tibble)
-importFrom(tibble,tibble)
 importFrom(tidyselect,starts_with)
 importFrom(utils,capture.output)
 importFrom(utils,head)

diff --git a/R/check_valid_ids.R b/R/check_valid_ids.R
@@ -1,26 +1,4 @@
-#' Check that NCBI IDs are valid
-#'
-#' \code{check_valid_ncbi_ids} checks that the NCBI IDs in a dataset from
-#' bugphyzz are valid.
-#'
-#' @param dat Dataset imported from bugphyzz.
-#'
-#' @return A dataframe with the positions and values that must be corrected,
-#' If no errors are found, the output is NULL.
-#'
-#' @importFrom magrittr %>%
-#' @importFrom taxizedb taxid2name
-#' @importFrom taxize classification
-#' @importFrom tibble tibble
-#' @importFrom dplyr bind_rows
-#' @importFrom tibble as_tibble
-#' @importFrom dplyr left_join
-#' @importFrom dplyr relocate
-#'
-#' @export
-#'
-check_valid_ncbi_ids <- function(dat) {
-
+.check_valid_ncbi_ids <- function(dat) {
   ncbi_ids <- dat[['NCBI_ID']]
   ncbi_ids <- ncbi_ids[!is.na(ncbi_ids)]
   ncbi_ids <- unique(as.character(ncbi_ids))

diff --git a/man/check_valid_ncbi_ids.Rd b/man/check_valid_ncbi_ids.Rd
diff --git a/vignettes/articles/checks.Rmd b/vignettes/articles/checks.Rmd
@@ -144,7 +144,7 @@ while taxizedb behaves like https://www.ncbi.nlm.nih.gov/taxonomy/.
 
 
 ```{r, message=FALSE, warning=FALSE, eval=FALSE}
-id_err <- lapply(phys, check_valid_ncbi_ids) %>% 
+id_err <- lapply(phys, bugphyzz:::.check_valid_ncbi_ids) %>% 
   purrr::discard(is.null) %>%
   bind_rows(.id = 'dataset')