ranking: Filter out species with too few species

man/optimal_weights.Rd

@@ -4,7 +4,13 @@
 \alias{optimal_weights}
 \title{Find the best weights to rank the results.}
 \usage{
-optimal_weights(analysis, methods, reference_gene_ids, target = "mean")
+optimal_weights(
+  analysis,
+  methods,
+  reference_gene_ids,
+  target = "mean",
+  min_n_species = 10
+)
 }
 \arguments{
 \item{analysis}{Results from \code{\link[=analyze]{analyze()}} or \code{\link[=ranking]{ranking()}}.}
@@ -15,6 +21,10 @@ optimal_weights(analysis, methods, reference_gene_ids, target = "mean")
 
 \item{target}{The optimization target. It may be one of "mean", "min" or
 "max" and results in the respective rank being optimized.}
+
+\item{min_n_species}{Minimum number of required species per gene. Genes that
+have fewer species will not be included in the rankings used to find the
+optimal weights.}
 }
 \value{
 Named list pairing method names with their optimal weights. This

man/ranking.Rd

@@ -4,13 +4,16 @@
 \alias{ranking}
 \title{Rank the results by computing a score.}
 \usage{
-ranking(analysis, weights)
+ranking(analysis, weights, min_n_species = 10)
 }
 \arguments{
 \item{analysis}{Analysis object resulting from \code{\link[=analyze]{analyze()}}.}
 
 \item{weights}{Named list pairing method names with weighting factors. Only
 methods that are contained within this list will be included.}
+
+\item{min_n_species}{Minimum number of required species per gene. Genes that
+have fewer species will not be included in the ranking.}
 }
 \value{
 A ranking object. The object extends the analysis result with