From 9ae95527f838d55c051824be6bf8e72a2e5902d0 Mon Sep 17 00:00:00 2001 From: moi-taiga Date: Tue, 19 Mar 2024 20:08:30 +0000 Subject: [PATCH] converted ensemble codes to gene symbols (allowing final plot to run) --- vignettes/BreastCancer.Rmd | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/vignettes/BreastCancer.Rmd b/vignettes/BreastCancer.Rmd index 86f2eef..0ec5478 100644 --- a/vignettes/BreastCancer.Rmd +++ b/vignettes/BreastCancer.Rmd @@ -163,6 +163,9 @@ sample.sce <- SingleCellExperiment(assays = list(expdata = sample.seu@assays$RNA #binarize the expression matrix (0.5 chosen as cutoff) sample.sce <- binarize_exp(sample.sce, fix_cutoff = TRUE, binarize_cutoff = 0.5) +#convert ensble gene names to gene symbols +rownames(sample.sce@assays@data@listData$binary) <- grch38$symbol[match(rownames(sample.sce), grch38$ensgene)] + # Filter the gene expression matrix for the switching genes sample_reduced <- ppr_filter_gene_expression_for_switching_genes(sample.sce@assays@data@listData$binary, bc_switching_genes) @@ -170,6 +173,7 @@ sample_reduced <- ppr_filter_gene_expression_for_switching_genes(sample.sce@assa # sample_reduced <- readRDS("~/Rprojects/BC/sample_reduced.rds") + #use ppr to predict the position of the exhausted cells sample.ppr <- ppr_predict_position(sample_reduced, reference.sg = bc_switching_genes)