combineGenes

NAMESPACE

@@ -8,6 +8,7 @@ export(checkEGGNOG)
 export(checkPATRIC)
 export(checkPATRICSimple)
 export(cnDiscretize)
+export(combineGenes)
 export(combineSeqs)
 export(compareGenes)
 export(consensusSeq)

R/combineGenes.R

@@ -0,0 +1,32 @@
+#' combineGenes
+#' 
+#' (experimental) use common genes across multiple datasets to
+#' merge gene copy numbers
+#' 
+#' @param stana_list stana list
+#' @param species species ID
+#' @export
+#' @return new stana object
+combineGenes <- function(stana_list, species, argList=list(), output_seq=FALSE) {
+  if (!is.list(stana_list)) {stop("Please provide list of stana object")}
+  each_ID <- lapply(stana_list, function(x) x@genes[[species]] |> row.names())
+  intersected <- Reduce(intersect, each_ID)
+  if (length(intersected)==0) {stop("No common genes")}
+
+  qqcat("Common genes: @{length(intersected)}\n")
+
+  merged <- do.call(cbind, lapply(stana_list, function(x) x@genes[[species]][intersected,]))
+
+  ## Metadata
+  new_stana <- new("stana")
+  new_stana@genes[[species]] <- merged
+  cls <- lapply(stana_list, function(x) x@cl)
+  cls <- do.call(c, cls)
+  new_stana@ids <- species
+  new_stana@type <- stana@type
+  new_stana@cl <- cls
+  new_stana@colors <- getColors(cls)
+
+  return(new_stana)
+}
+

R/compareGenes.R

@@ -14,9 +14,10 @@
 #' @export
 #' @return ggplot
 #' 
-compareGenes <- function(stana, species, geneID=NULL, cl=NULL, argList=list(),
+compareGenes <- function(stana, species=NULL, geneID=NULL, cl=NULL, argList=list(),
 	verbose_zero=FALSE) {
 	if (is.null(cl)) { cl <- stana@cl}
+	if (is.null(species)) {species <- stana@clearGenes[1]}
 	midas_merge_dir <- stana@mergeDir
 	geneDf <- stana@genes[[species]]
 	incSamples <- intersect(colnames(geneDf), unlist(cl))