diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml old mode 100755 new mode 100644 index 6ca9e4f..e7aa258 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ # R specific hooks: https://github.com/lorenzwalthert/precommit repos: - repo: https://github.com/lorenzwalthert/precommit - rev: v0.4.3.9015 + rev: v0.4.3.9026 hooks: - id: style-files args: [--style_pkg=styler, --style_fun=tidyverse_style] diff --git a/DESCRIPTION b/DESCRIPTION index 917c0a8..9b21732 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -14,7 +14,6 @@ Description: SimBu can be used to simulate bulk RNA-seq datasets with known cell License: GPL-3 + file LICENSE Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.3 Imports: basilisk, BiocParallel, @@ -46,3 +45,4 @@ VignetteBuilder: knitr Config/testthat/edition: 3 StagedInstall: no biocViews: Software, RNASeq, SingleCell +Config/roxygen2/version: 8.0.0 diff --git a/R/dataset.R b/R/dataset.R index 39e0d1d..26e2633 100755 --- a/R/dataset.R +++ b/R/dataset.R @@ -151,8 +151,6 @@ generate_summarized_experiment <- function(annotation, count_matrix, tpm_matrix, } - - #' Build \link[SummarizedExperiment]{SummarizedExperiment} using local annotation and count matrix R objects #' #' @param annotation (mandatory) dataframe; needs columns 'ID' and 'cell_type'; 'ID' needs to be equal with cell_names in count_matrix diff --git a/R/simulator.R b/R/simulator.R index c9b0e1f..a6dd338 100755 --- a/R/simulator.R +++ b/R/simulator.R @@ -837,7 +837,6 @@ merge_simulations <- function(simulation_list) { } - #' Create scaling vector from custom or pre-defined scaling factor #' #' @param data dataset diff --git a/man/SimBu.Rd b/man/SimBu.Rd index 2ebcbcf..5bf93f2 100755 --- a/man/SimBu.Rd +++ b/man/SimBu.Rd @@ -43,4 +43,9 @@ Useful links: \author{ \strong{Maintainer}: Alexander Dietrich \email{alex.dietrich@tum.de} +Authors: +\itemize{ + \item Alexander Dietrich \email{alex.dietrich@tum.de} +} + } diff --git a/tests/testthat/test_simulator.R b/tests/testthat/test_simulator.R index be14f20..df7560b 100755 --- a/tests/testthat/test_simulator.R +++ b/tests/testthat/test_simulator.R @@ -76,8 +76,6 @@ test_that("test different scaling factor calculations + mRNA bias removal from c }) - - test_that("test census", { tpm <- Matrix::Matrix(matrix(rpois(3e5, 5), ncol = 300), sparse = TRUE) tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm))