From 713679fbcb547c34bd8ca8958d8c1372c860e587 Mon Sep 17 00:00:00 2001 From: atpoint Date: Mon, 7 Oct 2024 14:24:08 +0200 Subject: [PATCH] retire unused argument --- DESCRIPTION | 2 +- NEWS | 8 +++++++- R/de_testing.R | 2 +- man/de_limma.Rd | 1 - 4 files changed, 9 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0bf9226..45c35f9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: SigGenes Title: Automated differential analysis and signature generation for bulk and single-cell data Description: Automated differential analysis between groups based on limma-voom and generation of per-group signatures via custom filtering. -Version: 1.0.5 +Version: 1.0.6 Author: Alexander Bender [aut,cre] Maintainer: Alexander Bender License: LGPL (>=2) diff --git a/NEWS b/NEWS index 1b481ab..05ee7d8 100644 --- a/NEWS +++ b/NEWS @@ -1,7 +1,13 @@ +CHANGES IN VERSION 1.0.6 +------------------------ + + o retire unused argument in `de_testing()` + + CHANGES IN VERSION 1.0.5 ------------------------ - o option to use limma-trend for testing rather than default limma-voom + o support to use limma-trend for testing via `use_trend=TRUE` CHANGES IN VERSION 1.0.4 diff --git a/R/de_testing.R b/R/de_testing.R index f4413ae..cae1dfa 100644 --- a/R/de_testing.R +++ b/R/de_testing.R @@ -84,7 +84,7 @@ #' @export de_limma <- function(x, use_assay = "counts", aggregate_by = NULL, use_existing_sf = TRUE, main_covariate, other_covariates = NULL, - test_method = c("trend", "voom"), block = NULL, + block = NULL, min_pct = 0, min_fc = 1.0, use_weights = FALSE, mode = c("pairwise", "average"), use_trend = FALSE, use_filterByExpr = FALSE, return_object = FALSE, delim = "_vs_") { diff --git a/man/de_limma.Rd b/man/de_limma.Rd index bee2e2d..9cffb62 100644 --- a/man/de_limma.Rd +++ b/man/de_limma.Rd @@ -11,7 +11,6 @@ de_limma( use_existing_sf = TRUE, main_covariate, other_covariates = NULL, - test_method = c("trend", "voom"), block = NULL, min_pct = 0, min_fc = 1,