From 86aae5589ef42bdb0996de8406a9d98233c028a2 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 6 Jul 2026 17:13:07 +0000 Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/lorenzwalthert/precommit: v0.4.3.9014 → v0.4.3.9026](https://github.com/lorenzwalthert/precommit/compare/v0.4.3.9014...v0.4.3.9026) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8740676..e7aa258 100644 --- 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: v0.4.3.9014 + rev: v0.4.3.9026 hooks: - id: style-files args: [--style_pkg=styler, --style_fun=tidyverse_style] From 6a3801f7c504a1b9dad1669e3d1d6902bfef6288 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 6 Jul 2026 17:16:16 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- R/BASE.R | 1 - R/custom_deconvolution_methods.R | 4 ---- R/estimate.R | 1 - R/immune_deconvolution_methods.R | 2 -- R/mouse_cell_type_mapping.R | 2 -- R/mouse_deconvolution_methods.R | 4 ---- tests/testthat/test_custom_matrices.R | 4 ---- 7 files changed, 18 deletions(-) diff --git a/R/BASE.R b/R/BASE.R index 1cec7bc..bbdfb1a 100644 --- a/R/BASE.R +++ b/R/BASE.R @@ -121,7 +121,6 @@ base_algorithm <- function(data, reg, perm = 100, median.norm = T) { } - #' Souce code to create the compendium used kin the BASE algorithm, containing #' up- and down-regulated weight sets that specify the # specificity by which each gene is expressed by a given cell. diff --git a/R/custom_deconvolution_methods.R b/R/custom_deconvolution_methods.R index 285cebf..9c5881a 100644 --- a/R/custom_deconvolution_methods.R +++ b/R/custom_deconvolution_methods.R @@ -15,7 +15,6 @@ NULL - #' List of methods that support the use of a custom signature #' #' The available methods are @@ -40,7 +39,6 @@ custom_deconvolution_methods <- c( ########################################################################### - #' Deconvolute using CIBERSORT or CIBERSORT abs and a custom signature matrix. #' #' @param gene_expression_matrix a m x n matrix with m genes and n samples @@ -127,8 +125,6 @@ deconvolute_epic_custom <- function(gene_expression_matrix, signature_matrix, } - - #' Deconvolute using ConsesnusTME and a custom signature matrix #' #' @param gene_expression_matrix a m x n matrix with m genes and n samples. Data diff --git a/R/estimate.R b/R/estimate.R index 119bd8d..9ebc99b 100644 --- a/R/estimate.R +++ b/R/estimate.R @@ -9,7 +9,6 @@ #' - #' ESTIMATE algortihm: This function computes stromal, immune, and ESTIMATE scores #' per sample using gene expression data, through GSEA. The ESTIMATE score is used #' to compute an estimate of the tumor purity diff --git a/R/immune_deconvolution_methods.R b/R/immune_deconvolution_methods.R index 551f268..5f01d17 100644 --- a/R/immune_deconvolution_methods.R +++ b/R/immune_deconvolution_methods.R @@ -73,7 +73,6 @@ set_cibersort_mat <- function(path) { } - ########################################################################### # Deconvolution functions for consistently accessing each method # @@ -380,7 +379,6 @@ deconvolute_consensus_tme <- function(gene_expression_matrix, } - #' Annotate unified cell_type names #' #' map the cell_types of the different methods to a common name diff --git a/R/mouse_cell_type_mapping.R b/R/mouse_cell_type_mapping.R index cbabf1b..6156c1f 100644 --- a/R/mouse_cell_type_mapping.R +++ b/R/mouse_cell_type_mapping.R @@ -54,8 +54,6 @@ reduce_mouse_cell_types <- function(deconvolution.results, } - - #' This function returns the list of all cell types in BASE/DCQ results, #' along with the cell type they are mapped to #' @param method the method for which we want to get the cell types diff --git a/R/mouse_deconvolution_methods.R b/R/mouse_deconvolution_methods.R index 5effa8a..da14d1e 100644 --- a/R/mouse_deconvolution_methods.R +++ b/R/mouse_deconvolution_methods.R @@ -34,8 +34,6 @@ deconvolution_methods_mouse <- c( ) - - ############################################################################ # Deconvolution functions for consistently accessing each method # @@ -45,7 +43,6 @@ deconvolution_methods_mouse <- c( ############################################################################ - #' Deconvolute using mMCP-counter #' #' @param gene_expression_matrix a m x n matrix with m genes and n samples. Should be TPM normalized @@ -202,7 +199,6 @@ deconvolute_base_algorithm <- function(gene_expression_matrix, n_permutations = } - #' Perform deconvolution on a mouse RNAseq dataset #' #' @param gene_expression_matrix a m x n matrix with m genes and n samples. diff --git a/tests/testthat/test_custom_matrices.R b/tests/testthat/test_custom_matrices.R index 9aeae65..bc6e1e0 100644 --- a/tests/testthat/test_custom_matrices.R +++ b/tests/testthat/test_custom_matrices.R @@ -4,7 +4,6 @@ test_mat <- read_tsv("bulk_mat.tsv") %>% test_mat <- as.matrix(test_mat) - test_that("seqimmucc works with a custom signature matrix", { test_mat <- dataset_racle$expr_mat sign_mat <- matrix(120 * runif(15000), ncol = 10) @@ -22,7 +21,6 @@ test_that("seqimmucc works with a custom signature matrix", { }) - test_that("EPIC works with a custom signature matrix", { sign_mat <- matrix(120 * runif(10 * nrow(test_mat)), ncol = 10) colnames(sign_mat) <- c( @@ -72,8 +70,6 @@ test_that("EPIC works with a custom signature matrix and variances", { }) - - test_that("ConsensusTME works with a custom signature matrix", { sign_mat <- matrix(120 * runif(1500), ncol = 10) colnames(sign_mat) <- c(