diff --git a/R/test_clustering_thresholds.R b/R/test_clustering_thresholds.R index f2e80da023333e12bf88880059bca62723e5e860..70f6b55a126c9663bcbe56b06878a5444ff1d4ac 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 88e2194527332181db60e8393bf5d32d376cd1a1..de5761e31d5630e67adc805a65b7e8d97e70b9f4 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.