AgglomClustering: AgglomClustering:
In nathansam/CircadianTools: Collection of Tools for Detecting Rhythmic Genes

Applies agglomerative hierarchical clustering to a transcriptomics dataset and appends a cluster column to this dataset for all genes.

AgglomClustering(
  dataset = NULL,
  distance = NULL,
  k = 10,
  metric = "euclidean",
  nthreads = NULL,
  scale = FALSE,
  center = TRUE
)

`dataset`	A transcriptomics dataset. First columns should be gene names. All other columns should be expression levels. Not needed if an argument to distance is given.
`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`	The total number of clusters.
`metric`	The distance metric to be used to calculate the distances between genes. See parallelDist::parDist for all accepted arguments.
`nthreads`	Number of processor threads to be used for calculating the distance matrix. If not specified then the maximum number of logical cores are used.
`scale`	If the gene activity should be scaled before clustering.
`center`	If the gene activity should be centered before clustering.