From 02556837137432c049b5c2c6bd4ac48df3512684 Mon Sep 17 00:00:00 2001 From: samuel-marsh Date: Thu, 5 Dec 2024 14:14:59 -0500 Subject: [PATCH] fix vignette errors --- vignettes/articles/LIGER_Functions.Rmd | 4 ++-- vignettes/articles/Object_Conversion.Rmd | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/vignettes/articles/LIGER_Functions.Rmd b/vignettes/articles/LIGER_Functions.Rmd index eb5ee70d1e..6c02321520 100644 --- a/vignettes/articles/LIGER_Functions.Rmd +++ b/vignettes/articles/LIGER_Functions.Rmd @@ -261,14 +261,14 @@ By default this will query all datasets in the object to create unified gene lis ```{r} gene_input_list <- c("P2ry12", "Fcrls", "Aif1") -genes_present <- Feature_Present(data = marsh_liger, gene_list = gene_input_list) +genes_present <- Feature_Present(data = marsh_liger, features = gene_input_list) ``` However you can check individual datasets within object by supplying those matrices to the `data` parameter. ```{r} gene_input_list <- c("P2ry12", "Fcrls", "Aif1") -genes_present <- Feature_Present(data = marsh_liger@raw.data[[1]], gene_list = gene_input_list) +genes_present <- Feature_Present(data = marsh_liger@datasets[[1]], features = gene_input_list) ``` diff --git a/vignettes/articles/Object_Conversion.Rmd b/vignettes/articles/Object_Conversion.Rmd index bef3da87fd..91239db233 100644 --- a/vignettes/articles/Object_Conversion.Rmd +++ b/vignettes/articles/Object_Conversion.Rmd @@ -59,7 +59,7 @@ Load Seurat Object & Add QC Data pbmc <- pbmc3k.SeuratData::pbmc3k.final pbmc <- UpdateSeuratObject(pbmc) -pbmc <- Add_Cell_QC_Metrics(seurat_object = pbmc, species = "human") +pbmc <- Add_Cell_QC_Metrics(object = pbmc, species = "human") ``` We'll also add some random meta data variables to pbmc data form use in this vignette