getter functions

DESCRIPTION

@@ -8,5 +8,5 @@ Authors@R: person("Noriaki", "Sato", email = "[email protected]", role = c("cre", "aut
 Depends: ggplot2, ggstar, ggraph, igraph
 Imports: GetoptLong, BiocFileCache, RCurl, igraph, vegan, methods, data.table, phangorn, RColorBrewer, ggtree, circlize, ComplexHeatmap, ggkegg, ape, dplyr, exactRankTests, ggblend, ggh4x, scales, tidygraph, ggplotify, ggtreeExtra, ggnewscale, scico, MKmisc
 Suggests: simplifyEnrichment, stringr, tidyr, Boruta, knitr, ggrepel
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr

NAMESPACE

@@ -29,7 +29,10 @@ export(genomeHeatmap)
 export(getAdonis)
 export(getCl)
 export(getFasta)
+export(getGeneID)
 export(getID)
+export(getKOID)
+export(getSNVID)
 export(getSlot)
 export(getTree)
 export(getTreePlot)
@@ -51,6 +54,7 @@ export(returnGenes)
 export(reverseAnnot)
 export(setAnnotation)
 export(setGroup)
+export(setMap)
 export(setMetadata)
 export(setTree)
 export(strainClusterHeatmap)

R/stana.R

@@ -123,6 +123,45 @@ setGeneric("getCl",
 setMethod("getCl", "stana",
     function(x) attr(x, "cl"))
 
+#' @export
+setGeneric("getGeneID",
+    function(x, candSp) standardGeneric("getGeneID"))
+
+setMethod("getGeneID", "stana",
+    function(x, candSp) {
+        if (is.null(stana@genes[[candSp]])) {
+            stop("No gene table available")
+        } else {
+            return(row.names(stana@genes[[candSp]]))
+        }
+})
+
+#' @export
+setGeneric("getSNVID",
+    function(x, candSp) standardGeneric("getSNVID"))
+
+setMethod("getSNVID", "stana",
+    function(x, candSp) {
+        if (is.null(stana@snps[[candSp]])) {
+            stop("No SNV table available")
+        } else {
+            return(row.names(stana@snps[[candSp]]))
+        }
+})
+
+#' @export
+setGeneric("getKOID",
+    function(x, candSp) standardGeneric("getKOID"))
+
+setMethod("getKOID", "stana",
+    function(x, candSp) {
+        if (is.null(stana@kos[[candSp]])) {
+            stop("No KO table available")
+        } else {
+            return(row.names(stana@kos[[candSp]]))
+        }
+})
+
 #' initializeStana
 #' @noRd
 initializeStana <- function(stana,cl) {