diff --git a/vignettes/memory.Rmd b/vignettes/memory.Rmd index fa21bb5..f7dda18 100644 --- a/vignettes/memory.Rmd +++ b/vignettes/memory.Rmd @@ -13,6 +13,7 @@ knitr::opts_chunk$set( collapse = TRUE, comment = "#>", echo = FALSE, + # eval = FALSE, message = FALSE, warning = FALSE ) @@ -41,15 +42,16 @@ metadat <- read_tsv(system.file( select(-sample_id) %>% rename(sample_id = barcode) renee_ds <- create_reneeDataSet_from_dataframes(metadat, counts) %>% - calc_cpm() %>% - filter_counts( - sample_names_column = "sample_id", - gene_names_column = "gene_id", - group_column = "treatments_radiation_treatment_type", - label_column = "sample", - columns_to_include = c("gene_id", metadat %>% pull("sample_id")), - make_plots = FALSE - ) + calc_cpm() +renee_ds@counts$filt <- renee_ds@counts$raw +# filter_counts( +# sample_names_column = "sample_id", +# gene_names_column = "gene_id", +# group_column = "treatments_radiation_treatment_type", +# label_column = "sample", +# columns_to_include = c("gene_id", metadat %>% pull("sample_id")), +# make_plots = FALSE +# ) ```