From 603e08ee139475cdc02fd70e6e6a2a2178ee1393 Mon Sep 17 00:00:00 2001 From: WackerO Date: Thu, 12 Oct 2023 11:25:47 +0200 Subject: [PATCH 1/2] added na.omit to assay reading --- R/accessory.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/accessory.R b/R/accessory.R index 5653e5b..bca49d5 100644 --- a/R/accessory.R +++ b/R/accessory.R @@ -789,7 +789,7 @@ read_matrix <- function(matrix_file, sample_metadata, feature_metadata = NULL, s } } - matrix_data <- as.matrix(matrix_data[, rownames(sample_metadata)]) + matrix_data <- na.omit(as.matrix(matrix_data[, rownames(sample_metadata)])) # Guess the log status From 797955cf6a16f6c15f42a0100e934b4a6c3a3b4e Mon Sep 17 00:00:00 2001 From: WackerO Date: Thu, 18 Jan 2024 09:08:10 +0100 Subject: [PATCH 2/2] Small pval_column bugfix --- exec/validate_fom_components.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/exec/validate_fom_components.R b/exec/validate_fom_components.R index aa0e3fc..9379b9a 100755 --- a/exec/validate_fom_components.R +++ b/exec/validate_fom_components.R @@ -116,7 +116,7 @@ validated_parts <- validate_inputs( sample_id_col = opt$sample_id_col, feature_id_col = opt$feature_id_col, differential_results = opt$differential_results, - pval_column = opt$feature_id_col, + pval_column = opt$pval_column, qval_column = opt$qval_column, fc_column = opt$fold_change_column, unlog_foldchanges = opt$unlog_foldchanges