From 646fb01716f53b71e8ce43c46ccfe0f65cff3bd7 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Tue, 8 Oct 2024 11:42:07 -0400 Subject: [PATCH] docs: demo filter_counts() in intro vignette --- vignettes/intro.Rmd | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/vignettes/intro.Rmd b/vignettes/intro.Rmd index 07fb002..65094c2 100644 --- a/vignettes/intro.Rmd +++ b/vignettes/intro.Rmd @@ -35,5 +35,14 @@ renee_ds <- create_reneeDataSet_from_files( gene_counts_filepath = gene_counts_tsv ) -renee_ds@counts$raw %>% head() +renee_ds <- renee_ds %>% filter_counts( + group_column = "condition", + label_column = "sample_id", + columns_to_include = c("gene_id", "KO_S3", "KO_S4", "WT_S1", "WT_S2"), + minimum_count_value_to_be_considered_nonzero = 1, + minimum_number_of_samples_with_nonzero_counts_in_total = 1, + minimum_number_of_samples_with_nonzero_counts_in_a_group = 1, +) + +renee_ds@counts$filt %>% head() ```