ClusterParamSelection: ClusterParamSelection

Description Usage Arguments Examples

View source: R/cluster_param_selection.R

Description

Calculates validation metrics for different clustering methods and different numbers of partitions. The validation metrics are plotted.

Usage

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ClusterParamSelection(
  dataset = NULL,
  distance = NULL,
  k = c(2, 5, 10),
  method = c("pam", "agglom", "diana"),
  metric = "euclidean",
  scale = TRUE,
  nthreads = 2,
  save.plot = TRUE,
  save.df = TRUE,
  path = NULL
)

Arguments

dataset

A transcriptomics dataset. Preferably filtered first. First columns should be gene names. All other columns should be expression levels.

distance

A distance matrix. If a distance matrix has already been created (such as by using the DistanceGen function), the matrix can be passed to this function to save time. If a distance matrix is not provided then it will be generated by the function.

k

A numeric vector giving the number of clusters to be evaluated.

method

The clustering method(s) to be used. Multiple methods can be considered by providing a character vector. Currently accepts 'pam', 'agglom' and 'diana'.

metric

The distance metric to be used to calculate the distances between genes. See parallelDist::parDist for all accepted arguments. Also allows the option of 'abs.correlation'. Not used if a distance matrix is provided.

scale

Logical. If TRUE then each gene will be scaled.

nthreads

The number of threads to be used for parallel computations. If NULL then the maximum number of threads available will be used.

save.plot

Logical. If TRUE then saves the plots generated.

save.df

Logical. If TRUE then saves the validation metric results as a .csv file.

path

The directory to be used for saving plots and the validation metric results to. Uses the name of the dataset object appended with '_validation' if this argument is not specified.

Examples

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k.options <- seq(2,10)
hclust.validation <- ClusterParamSelection(Laurasmappings, k=k.options,
                                           nthreads = 2)

nathansam/CircadianTools documentation built on Dec. 26, 2019, 11:30 a.m.