From 8b0763780c5b012653380fbb6a3ad4e93d35a586 Mon Sep 17 00:00:00 2001 From: aduvermy <arnaud.duvermy@ens-lyon.fr> Date: Tue, 2 Apr 2024 14:43:02 +0200 Subject: [PATCH] add check for <countMatrix> and <metadata> dimensions Former-commit-id: f66936e5b1ee6ea63b9b15054f87b2916494c8e8 Former-commit-id: 3eedbea70438a57a7828338fdabc6909be139092 Former-commit-id: 3ba2e32df23e2849a7e2cd1bd6bd82f6dfc3f198 --- R/prepare_data2fit.R | 2 ++ dev/flat_full.Rmd | 2 ++ vignettes/02-tutorial.Rmd | 1 - 3 files changed, 4 insertions(+), 1 deletion(-) diff --git a/R/prepare_data2fit.R b/R/prepare_data2fit.R index e10e1fd..660e3de 100644 --- a/R/prepare_data2fit.R +++ b/R/prepare_data2fit.R @@ -142,6 +142,8 @@ custom_matrix_transform <- function(count_matrix, custom_expression) { prepareData2fit <- function(countMatrix, metadata, response_name = "kij", groupID = "geneID", row_threshold = 0, transform = NULL , normalization = NULL) { + ## -- first check + stopifnot("<countMatrix> and <metadata> dimensions do not match!" = dim(countMatrix)[2] == dim(metadata)[1] ) stopifnot( length(row_threshold) == 1 && is.numeric(row_threshold) && row_threshold >= 0 ) if (row_threshold > 0){ diff --git a/dev/flat_full.Rmd b/dev/flat_full.Rmd index 742804c..b9d8dc1 100644 --- a/dev/flat_full.Rmd +++ b/dev/flat_full.Rmd @@ -2801,6 +2801,8 @@ custom_matrix_transform <- function(count_matrix, custom_expression) { prepareData2fit <- function(countMatrix, metadata, response_name = "kij", groupID = "geneID", row_threshold = 0, transform = NULL , normalization = NULL) { + ## -- first check + stopifnot("<countMatrix> and <metadata> dimensions do not match!" = dim(countMatrix)[2] == dim(metadata)[1] ) stopifnot( length(row_threshold) == 1 && is.numeric(row_threshold) && row_threshold >= 0 ) if (row_threshold > 0){ diff --git a/vignettes/02-tutorial.Rmd b/vignettes/02-tutorial.Rmd index 966cd96..3eeb443 100644 --- a/vignettes/02-tutorial.Rmd +++ b/vignettes/02-tutorial.Rmd @@ -15,7 +15,6 @@ knitr::opts_chunk$set( ``` ```{r setup} -devtools::load_all() library(HTRfit) ``` -- GitLab