1. vsclust
  2. man
  3. runClustWrapper.Rd
Browse code

fixes of all kinds for passing checks

veitveit authored on 13/11/2024 19:53:08
Showing 1 changed files
man/runClustWrapper.Rd
History View file @ 30dbbfe
... ... 
@@ -9,6 +9,7 @@ runClustWrapper(
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   NClust,
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   proteins = NULL,
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   VSClust = TRUE,
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+  scaling = "standardize",
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   cores,
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   verbose = FALSE
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 )
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@@ -24,6 +25,9 @@ to be added to the results}
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 \item{VSClust}{boolean. TRUE for running the variance-sensitive clustering.
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 Otherwise, the function will call standard fuzzy c-means clustering}
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+\item{scaling}{Either `standardize` (default), `center` or `none`. Standardized
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+features get mean 0 and standard deviation 1. Centered samples get mean 0.}
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+
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 \item{cores}{Number of threads for the parallelization}
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 \item{verbose}{Show more information during execution}
Browse code

speedup of algorithm

veitveit authored on 26/01/2023 08:06:40
Showing 1 changed files
man/runClustWrapper.Rd
History View file @ 771a6a9
... ... 
@@ -4,7 +4,14 @@
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 \alias{runClustWrapper}
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 \title{Wrapper for running cluster analysis}
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 \usage{
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-runClustWrapper(dat, NClust, proteins = NULL, VSClust = TRUE, cores)
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+runClustWrapper(
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+  dat,
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+  NClust,
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+  proteins = NULL,
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+  VSClust = TRUE,
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+  cores,
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+  verbose = FALSE
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+)
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 }
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 \arguments{
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 \item{dat}{matrix or data frame with feature values for different conditions}
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@@ -18,6 +25,8 @@ to be added to the results}
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 Otherwise, the function will call standard fuzzy c-means clustering}
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 \item{cores}{Number of threads for the parallelization}
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+
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+\item{verbose}{Show more information during execution}
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 }
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 \value{
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 list with the items `dat`(the original data), `Bestcl` clustering
Browse code

added now function for biocondcutor and many fixes

Veit Schwammle authored on 23/09/2022 11:37:56
Showing 1 changed files
man/runClustWrapper.Rd
History View file @ b634e98
... ... 
@@ -1,5 +1,5 @@
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 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/HelperFuncs.R
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+% Please edit documentation in R/WrapperFuncs.R
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 \name{runClustWrapper}
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 \alias{runClustWrapper}
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 \title{Wrapper for running cluster analysis}
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@@ -11,21 +11,27 @@ runClustWrapper(dat, NClust, proteins = NULL, VSClust = TRUE, cores)
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 \item{NClust}{Number of cluster for running the clustering}
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-\item{proteins}{vector with additional feature information (default is NULL) to be added to the results}
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+\item{proteins}{vector with additional feature information (default is NULL)
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+to be added to the results}
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-\item{VSClust}{boolean. TRUE for running the variance-sensitive clustering. Otherwise, the function will call standard fuzzy c-means clustering}
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+\item{VSClust}{boolean. TRUE for running the variance-sensitive clustering.
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+Otherwise, the function will call standard fuzzy c-means clustering}
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 \item{cores}{Number of threads for the parallelization}
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 }
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 \value{
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-list with the items `dat`(the original data), `Bestcl` clustering results (same as from vsclust_algorithm), `p` (plot object with mfuzz plots), `outFileClust`(suitable matrix with complete information) , `ClustInd` (information about being member of any cluster, feature needs on membership values > 0.5)
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+list with the items `dat`(the original data), `Bestcl` clustering
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+results (same as from vsclust_algorithm), `p` (plot object with mfuzz plots),
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+`outFileClust`(suitable matrix with complete information) , `ClustInd`
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+(information about being member of any cluster, feature needs on membership
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+values > 0.5)
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 }
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 \description{
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 This function runs the clustering and visualizes the results.
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 }
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 \examples{
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 data(iris)
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-data <- cbind(iris[,1:4],1)
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+data <- cbind(iris[,seq_len(4)],1)
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 clust_out <- runClustWrapper(data, NClust=3, cores=1)
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 clust_out$p
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 }
Browse code

ready for bioconductor

veitveit authored on 18/07/2022 11:59:30
Showing 1 changed files
man/runClustWrapper.Rd
History View file @ ad4be2b
... ... 
@@ -4,7 +4,7 @@
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 \alias{runClustWrapper}
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 \title{Wrapper for running cluster analysis}
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 \usage{
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-runClustWrapper(dat, NClust, proteins = NULL, VSClust = T, cores)
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+runClustWrapper(dat, NClust, proteins = NULL, VSClust = TRUE, cores)
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 }
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 \arguments{
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 \item{dat}{matrix or data frame with feature values for different conditions}
Browse code

progressing

veitveit authored on 17/07/2022 08:25:08
Showing 1 changed files
man/runClustWrapper.Rd
History View file @ aaea0fd
... ... 
@@ -2,10 +2,30 @@
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 % Please edit documentation in R/HelperFuncs.R
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 \name{runClustWrapper}
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 \alias{runClustWrapper}
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-\title{Wrapper for clustering}
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+\title{Wrapper for running cluster analysis}
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 \usage{
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 runClustWrapper(dat, NClust, proteins = NULL, VSClust = T, cores)
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 }
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+\arguments{
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+\item{dat}{matrix or data frame with feature values for different conditions}
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+
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+\item{NClust}{Number of cluster for running the clustering}
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+
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+\item{proteins}{vector with additional feature information (default is NULL) to be added to the results}
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+
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+\item{VSClust}{boolean. TRUE for running the variance-sensitive clustering. Otherwise, the function will call standard fuzzy c-means clustering}
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+
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+\item{cores}{Number of threads for the parallelization}
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+}
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+\value{
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+list with the items `dat`(the original data), `Bestcl` clustering results (same as from vsclust_algorithm), `p` (plot object with mfuzz plots), `outFileClust`(suitable matrix with complete information) , `ClustInd` (information about being member of any cluster, feature needs on membership values > 0.5)
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+}
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 \description{
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-Wrapper for clustering
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+This function runs the clustering and visualizes the results.
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+}
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+\examples{
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+data(iris)
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+data <- cbind(iris[,1:4],1)
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+clust_out <- runClustWrapper(data, NClust=3, cores=1)
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+clust_out$p
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 }
Browse code

now full R package

veitveit authored on 23/03/2022 18:24:24
Showing 1 changed files
man/runClustWrapper.Rd
History View file @ 48d270b
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new file mode 100644
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@@ -0,0 +1,11 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/HelperFuncs.R
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+\name{runClustWrapper}
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+\alias{runClustWrapper}
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+\title{Wrapper for clustering}
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+\usage{
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+runClustWrapper(dat, NClust, proteins = NULL, VSClust = T, cores)
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+}
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+\description{
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+Wrapper for clustering
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+}