Commit 61eeb35e authored by domingue's avatar domingue
Browse files

Change to make sure it passes devtools::check locally

parent 7ccf4607
Pipeline #1725 failed with stage
in 43 minutes and 30 seconds
......@@ -42,12 +42,12 @@ Imports:
plyr (>= 1.8.0),
magrittr (>= 1.5),
prettycode (>= 1.0.0),
assertthat (>= 0.2.0),
knitr (>= 1.20),
biomaRt
Suggests:
knitr (>= 1.20),
rmarkdown (>= 1.10),
testthat (>= 2.1.0),
assertthat (>= 0.2.0),
org.Hs.eg.db (>= 3.8.2),
org.Mm.eg.db (>= 3.8.2),
org.Dr.eg.db (>= 3.8.2),
......
......@@ -82,11 +82,16 @@ importFrom(BiocManager,available)
importFrom(BiocManager,install)
importFrom(ReactomePA,enrichPathway)
importFrom(assertthat,assert_that)
importFrom(biomaRt,getBM)
importFrom(biomaRt,listMarts)
importFrom(biomaRt,useDataset)
importFrom(biomaRt,useMart)
importFrom(clusterProfiler,bitr)
importFrom(clusterProfiler,enrichGO)
importFrom(clusterProfiler,enrichKEGG)
importFrom(dplyr,bind_rows)
importFrom(dplyr,filter)
importFrom(dplyr,filter_)
importFrom(dplyr,groups)
importFrom(dplyr,if_else)
importFrom(dplyr,mutate)
......@@ -94,6 +99,7 @@ importFrom(dplyr,n)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,summarize)
importFrom(dplyr,tbl_df)
importFrom(forcats,fct_infreq)
importFrom(forcats,fct_rev)
importFrom(knitr,kable)
......@@ -103,14 +109,18 @@ importFrom(rlang,enquo)
importFrom(rlang,get_expr)
importFrom(rlang,quo_name)
importFrom(stringr,str_detect)
importFrom(stringr,str_extract)
importFrom(stringr,str_length)
importFrom(stringr,str_match)
importFrom(stringr,str_replace)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_sub)
importFrom(tibble,as_tibble)
importFrom(tibble,data_frame)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,gather)
importFrom(tidyr,nest)
importFrom(tidyr,unnest)
importFrom(utils,packageVersion)
importFrom(utils,page)
......@@ -81,7 +81,7 @@ vec2df <- function(namedVec) {
#'
#' @return a data.frame
#'
#' @importFrom tibble tibble
#' @importFrom tibble tibble rownames_to_column
#'
#' @export
#'
......
......@@ -133,7 +133,8 @@ as_int_matrix <- function(x) {
#'
#' @return a tibble
#'
#' @importFrom tibble tbl_df rownames_to_column
#' @importFrom dplyr tbl_df
#' @importFrom tibble rownames_to_column
#' @importFrom tidyr gather
#'
#' @export
......@@ -152,7 +153,7 @@ as_int_matrix <- function(x) {
expr_matrix_to_df <- function(m, id = "gene_id") {
m %>%
as_df() %>%
tibble::tbl_df() %>%
dplyr::tbl_df() %>%
tibble::rownames_to_column(id) %>%
tidyr::gather(replicate, expression, -one_of(id))
}
......
......@@ -18,7 +18,7 @@ A matrix
Wrapper for \code{\link[cummeRbund:repFpkmMatrix]{cummeRbund::repFpkmMatrix()}} and \code{\link[corescf:filterByExpression]{corescf::filterByExpression()}}
}
\note{
cummeRbund is now very old and has been superseded by better tools. It should no be the first choice for analysis.
cummeRbund is now very old and has been superseded by better tools. It should not be the first choice for gene expression analysis.
}
\examples{
\dontrun{
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment