clusterSamples {methylKit} | R Documentation

## Hierarchical Clustering using methylation data The function clusters samples using `hclust` function and various distance metrics derived from percent methylation per base or per region for each sample.

### Description

Hierarchical Clustering using methylation data

The function clusters samples using `hclust` function and various distance metrics derived from percent methylation per base or per region for each sample.

### Usage

    clusterSamples(.Object, dist="correlation", method="ward",
                           sd.filter=TRUE,sd.threshold=0.5,
                           filterByQuantile=TRUE, plot=TRUE,chunk.size)

    ## S4 method for signature 'methylBase'
    clusterSamples(
      .Object,
      dist,
      method,
      sd.filter,
      sd.threshold,
      filterByQuantile,
      plot
    )

    ## S4 method for signature 'methylBaseDB'
    clusterSamples(
      .Object,
      dist = "correlation",
      method = "ward",
      sd.filter = TRUE,
      sd.threshold = 0.5,
      filterByQuantile = TRUE,
      plot = TRUE,
      chunk.size = 1e+06
    )

### Arguments

`.Object` | a `methylBase` or `methylBaseDB` object
`dist` | the distance measure to be used. This must be one of "`correlation`", "`euclidean`", "`maximum`", "`manhattan`", "`canberra`", "`binary`" or "`minkowski`". Any unambiguous abbreviation can be given. (default:"`correlation`")
`method` | the agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "`ward.D`", "`ward.D`", "`single`", "`complete`", "`average`", "`mcquitty`", "`median`" or "`centroid`". (default:"`ward`")
`sd.filter` | If `TRUE`, the bases/regions with low variation will be discarded prior to clustering (default:TRUE)
`sd.threshold` | A numeric value. If `filterByQuantile` is `TRUE`, features whose standard deviations is less than the quantile denoted by `sd.threshold` will be removed. If `filterByQuantile` is `FALSE`, then features whose standard deviations is less than the value of `sd.threshold` will be removed.(default:0.5)
`filterByQuantile` | A logical determining if `sd.threshold` is to be interpreted as a quantile of all Standard Deviation values from bases/regions (the default), or as an absolute value
`plot` | a logical value indicating whether to plot hierarchical clustering. (default:TRUE)
`chunk.size` | Number of rows to be taken as a chunk for processing the `methylBaseDB` objects, default: 1e6

### Value

a `tree` object of a hierarchical cluster analysis using a set of dissimilarities for the n objects being clustered.

### Details

The parameter `chunk.size` is only used when working with `methylBaseDB` objects, as they are read in chunk by chunk to enable processing large-sized objects which are stored as flat file database. Per default the chunk.size is set to 1M rows, which should work for most systems. If you encounter memory problems or have a high amount of memory available feel free to adjust the `chunk.size`.

### Examples

    data(methylKit)

    clusterSamples(methylBase.obj, dist="correlation", method="ward", plot=TRUE)

[Package methylKit version 1.14.2 Index]