number_clusters {multiClust} | R Documentation |
Function to determine the number of clusters to be used to cluster gene probes and samples.
number_clusters(data.exp, Fixed = 3, gap_statistic = NULL)
data.exp |
The numeric original gene expression matrix to be used for clustering of genes and samples. This object is an output of the input_file function. |
Fixed |
A positive integer used to represent the number of clusters the samples and probes will be divided into. The default cluster number is set to 3 clusters. |
gap_statistic |
A logical indicating whether to use the gap_statistic to determine the optimal number of clusters to divide samples into. |
An object with the determined number of clusters to use.
The user should only choose either the fixed or gap_statistic option, not both. When using the gap_statistic option, change the argument to TRUE and "Fixed" to NULL.
Nathan Lawlor, Alec Fabbri
#Example 1: Using a fixed cluster number # Load in a test file data_file <- system.file("extdata", "GSE2034.normalized.expression.txt", package="multiClust") data <- input_file(data_file) clust_num <- number_clusters(data.exp=data, Fixed=3, gap_statistic=NULL) ## Not run: # Example 2: Using the gap_statistic to determine the optimal cluster number # Computation time is somewhat long clust_num <- number_clusters(data.exp=data, Fixed=NULL, gap_statistic=TRUE) ## End(Not run)