From 0291eca2a4f352e929c187b5fb2743adc4cfb1c3 Mon Sep 17 00:00:00 2001
From: olapuente <o.lapuente.santana@tue.nl>
Date: Tue, 16 May 2023 13:13:47 +0200
Subject: [PATCH] Removed NA LR pairs

---
 vignettes/easier_user_manual.Rmd | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/vignettes/easier_user_manual.Rmd b/vignettes/easier_user_manual.Rmd
index 2f2b681..ad51896 100644
--- a/vignettes/easier_user_manual.Rmd
+++ b/vignettes/easier_user_manual.Rmd
@@ -269,7 +269,12 @@ More detailed information on how these networks were obtained can be found in th
 ```{r, eval=TRUE}
 lrpair_weights <- compute_LR_pairs(RNA_tpm = RNA_tpm,
                                    cancer_type = "pancan")
+
+# Remove LR which are not found (NA's)
+na_lrpairs <- names(lrpair_weights)[is.na(apply(lrpair_weights, 2, sum))]
+lrpair_weights <- lrpair_weights[, -which(colnames(lrpair_weights) %in% na_lrpairs)]
 head(lrpair_weights[,1:5])
+
 ```
 
 Via `cancer_type`, a cancer-specific ligand-receptor pairs network can be chosen. With `cancer_type` set to `pancan`, a pan-cancer network will be used and this is based on the union of all ligand-receptor pairs present across the 18 cancer-specific networks.