From 206c3849d1a3408be15d0523f2135ae68eaf4e68 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 17 Nov 2023 16:06:01 +0000 Subject: [PATCH 1/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- R/custom_deconvolution_methods.R | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/R/custom_deconvolution_methods.R b/R/custom_deconvolution_methods.R index c7b48fa..add66ae 100644 --- a/R/custom_deconvolution_methods.R +++ b/R/custom_deconvolution_methods.R @@ -165,7 +165,6 @@ deconvolute_consensus_tme_custom <- function(gene_expression_matrix, signature_g deconvolute_seqimmucc_custom <- function(gene_expression_matrix, signature_matrix, ...) { - arguments <- dots_list( signature = signature_matrix, SampleData = gene_expression_matrix, ..., .homonyms = "last" @@ -175,7 +174,7 @@ deconvolute_seqimmucc_custom <- function(gene_expression_matrix, results <- eval(call) - #results <- seqImmuCC_LLSR(signature_matrix, gene_expression_matrix, ..., .homonyms = "last") + # results <- seqImmuCC_LLSR(signature_matrix, gene_expression_matrix, ..., .homonyms = "last") results <- results[, !colnames(results) %in% c("Correlation", "RMSE")] return(t(results)) From 5f4dc80fde63975037705fe7ecc787e6b7761ddb Mon Sep 17 00:00:00 2001 From: LorenzoMerotto Date: Fri, 17 Nov 2023 16:08:49 +0000 Subject: [PATCH 2/2] Roxygenize --- man/deconvolute_seqimmucc_custom.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/man/deconvolute_seqimmucc_custom.Rd b/man/deconvolute_seqimmucc_custom.Rd index dff6d3b..fb035ce 100644 --- a/man/deconvolute_seqimmucc_custom.Rd +++ b/man/deconvolute_seqimmucc_custom.Rd @@ -13,7 +13,7 @@ should be TPM normalized and log10 scaled.} \item{signature_matrix}{a m x l matrix with m genes and l cell types. The matrix should contain only a subset of the genes useful for the analysis.} -\item{...}{passed to the original seqImmuCC_LLSR fnuction} +\item{...}{passed to the original seqImmuCC_LLSR function} } \description{ Deconvolute using seqImmuCC (LLSR regression) and a custom signature matrix