From f695201de76ffb16f6f9d8b5cd7161d4e57cfb8d Mon Sep 17 00:00:00 2001 From: Simeon <51403284+simeross@users.noreply.github.com> Date: Fri, 26 Jan 2024 14:08:57 +0100 Subject: [PATCH] add vararg to threshold testing --- R/test_clustering_thresholds.R | 5 +++-- man/test_clustering_thresholds.Rd | 5 ++++- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/R/test_clustering_thresholds.R b/R/test_clustering_thresholds.R index f2e80da..70f6b55 100644 --- a/R/test_clustering_thresholds.R +++ b/R/test_clustering_thresholds.R @@ -12,6 +12,7 @@ #' running `which meshclust`, see also \code{\link{meshclustR}}. #' @param meshclust_temp_dir temporary directory for meshclust files. #' Temporary files will be removed after running the function. +#' @param ... pass on any additional strings to the meshclust commandline tool. #' #' @return A list of clustering results, where each element in the list corresponds to a specific threshold value. #' @@ -29,7 +30,7 @@ test_clustering_thresholds <- function(MyDNAstring, step_size, step_max = 0.99, ncores = 1, method = "Clusterize", - meshclust_temp_dir = "tmp") { + meshclust_temp_dir = "tmp", ...) { if(method == "Clusterize"){ #DECIPHER removed the 'type' argument from IdClusters around v2.24. Currently (Feb23), the function is renamed "Clusterize" @@ -56,7 +57,7 @@ test_clustering_thresholds <- function(MyDNAstring, step_size, clus_tbl_list <- lapply(seq(0, step_max, step_size), meshclustR, seqs = MyDNAstring, filepath = meshclust_temp_dir, - meshclust_bin = method) + meshclust_bin = method, ...) if(!preexisting){ unlink(meshclust_temp_dir) } diff --git a/man/test_clustering_thresholds.Rd b/man/test_clustering_thresholds.Rd index 88e2194..de5761e 100644 --- a/man/test_clustering_thresholds.Rd +++ b/man/test_clustering_thresholds.Rd @@ -10,7 +10,8 @@ test_clustering_thresholds( step_max = 0.99, ncores = 1, method = "Clusterize", - meshclust_temp_dir = "tmp" + meshclust_temp_dir = "tmp", + ... ) } \arguments{ @@ -28,6 +29,8 @@ running `which meshclust`, see also \code{\link{meshclustR}}.} \item{meshclust_temp_dir}{temporary directory for meshclust files. Temporary files will be removed after running the function.} + +\item{...}{pass on any additional strings to the meshclust commandline tool.} } \value{ A list of clustering results, where each element in the list corresponds to a specific threshold value. -- GitLab