From 934aaf69104b0b9a6f2735ca5bad19785f6dc07b Mon Sep 17 00:00:00 2001
From: Ivo Kwee <ivo.kwee@gmail.com>
Date: Fri, 22 Dec 2023 14:32:33 +0100
Subject: [PATCH 1/2] update

---
 NAMESPACE | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/NAMESPACE b/NAMESPACE
index 759a08b8..2941927d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -141,9 +141,11 @@ export(ngs.fitContrastsWithAllMethods)
 export(ngs.fitContrastsWithEDGER)
 export(ngs.fitContrastsWithLIMMA)
 export(ngs.fitContrastsWithTTEST)
+export(ngs.getGeneAnnot)
 export(ngs.getGeneAnnotation)
 export(ngs.getGeneAnnotation_DEPRECATED)
 export(ngs.save)
+export(ngs.tximportSalmon)
 export(nmfImpute)
 export(normalizeCounts)
 export(normalizeRLE)

From cab576e6bea91325db9b7e1d8e63c8d90f34df78 Mon Sep 17 00:00:00 2001
From: Ivo Kwee <ivo.kwee@gmail.com>
Date: Fri, 22 Dec 2023 15:42:08 +0100
Subject: [PATCH 2/2] fix: not parsing ensemble with dot-version (critical)

---
 R/pgx-compute.R |  1 -
 R/pgx-ensembl.R | 31 ++++++++++++++++++++++++-------
 2 files changed, 24 insertions(+), 8 deletions(-)

diff --git a/R/pgx-compute.R b/R/pgx-compute.R
index 0b479d1d..493bb53d 100644
--- a/R/pgx-compute.R
+++ b/R/pgx-compute.R
@@ -171,7 +171,6 @@ pgx.createPGX <- function(counts,
   message("[createPGX] input: dim(samples) = ", paste(dim(samples), collapse = "x"))
   message("[createPGX] input: dim(contrasts) = ", paste(dim(contrasts), collapse = "x"))
 
-
   ## convert old-style contrast matrix to sample-wise labeled contrasts
   contrasts <- playbase::contrasts.convertToLabelMatrix(contrasts, samples)
 
diff --git a/R/pgx-ensembl.R b/R/pgx-ensembl.R
index 90c0e215..6b4f9035 100644
--- a/R/pgx-ensembl.R
+++ b/R/pgx-ensembl.R
@@ -446,22 +446,27 @@ pgx.gene_table <- function(pgx, organism) {
 #' @export
 detect_probe_DEPRECATED <- function(probes, organism) {
   # Get org database
-  if (organism == "Human") {
+  if (tolower(organism) == "human") {
     org_db <- org.Hs.eg.db::org.Hs.eg.db
-  } else if (organism == "Mouse") {
+  } else if (tolower(organism) == "mouse") {
     org_db <- org.Mm.eg.db::org.Mm.eg.db
-  } else if (organism == "Rat") {
+  } else if (tolower(organism) == "rat") {
     org_db <- org.Rn.eg.db::org.Rn.eg.db
   }
 
   # Probe types
   keytypes <- c(
-    "ENSEMBL", "ENSEMBLTRANS", "SYMBOL",
-    "REFSEQ", "UNIPROT", "ACCNUM"
+    "ENSEMBL", "ENSEMBLTRANS", "SYMBOL", "REFSEQ", "UNIPROT", "ACCNUM"
   )
-  key_matches <- vector("character", length(keytypes))
+  ##  key_matches <- vector("character", length(keytypes))
+  key_matches <- rep( 0L, length(keytypes))
   names(key_matches) <- keytypes
 
+  ## discard version numbers if ENSEMBL
+  if(mean(grepl("^ENS",probes)) > 0.8) {
+    probes <- sub("[.][0-9]+", "", probes)
+  }
+  
   # Subset probes if too many
   if (length(probes) > 100) {
     probes <- probes[as.integer(seq(1, length(probes), 100))]
@@ -516,7 +521,8 @@ detect_probe_DEPRECATED <- function(probes, organism) {
 #' }
 #' @export
 ngs.getGeneAnnotation_DEPRECATED <- function(probes, probe_type, organism) {
-  # Get org database and columns request
+
+                                        # Get org database and columns request
   if (organism == "Human") {
     org_db <- org.Hs.eg.db::org.Hs.eg.db
     cols_req <- c("SYMBOL", "GENENAME", "CHR", "CHRLOC", "MAP", "GENETYPE")
@@ -528,6 +534,12 @@ ngs.getGeneAnnotation_DEPRECATED <- function(probes, probe_type, organism) {
     cols_req <- c("SYMBOL", "GENENAME", "CHR", "CHRLOC", "GENETYPE")
   }
 
+  ## discard version numbers if ENSEMBL
+  orig.probes <- probes
+  if(mean(grepl("^ENS",probes)) > 0.8) {
+    probes <- sub("[.][0-9]+", "", probes)
+  }
+  
   # Call for annotation table
   suppressWarnings(d <- AnnotationDbi::select(org_db,
     keys = probes,
@@ -544,6 +556,11 @@ ngs.getGeneAnnotation_DEPRECATED <- function(probes, probe_type, organism) {
     d$MAP <- d$CHR
   }
 
+  ## if ENSEMBL get original probe names with version
+  if(probe_type == "ENSEMBL") {
+    d$ENSEMBL <- orig.probes[match(d$ENSEMBL, probes)]
+  }
+  
   # Rename cols, add extra cols, reorder cols and rows
   if (probe_type == "SYMBOL") {
     d[, feature := SYMBOL]