cmdsFit

cmdsFit-methods

cmdsFit,matrix-method

 Dimensionality of the reconstructed space, typically set to 2
  or 3.

 Set to <code>"classic"</code> to perform classical MDS (uses
  function <code>cmdscale</code> from package <code>stats</code>). Set to
  <code>"isoMDS"</code> to use Kruskal's non-metric MDS (uses function
  <code>isoMDS</code> from package <code>MASS</code>). 

type

 Logical indicating if an additive constant c* should be
          computed, and added to the non-diagonal dissimilarities such
          that all n-1 eigenvalues are non-negative in <code>cmdscale</code> 

 A character string indicating which correlation
  coefficient (or covariance) is to be computed.  One of "pearson"
  (default), "kendall", or "spearman", can be abbreviated.

cor.method


<code>cmdsFit</code> obtains coordinates in a <code>k</code> dimensional space
which best approximate the given distances between objects.


 graphs

We provide efficient, easy-to-use tools for
High-Throughput Sequencing (ChIP-seq, RNAseq etc.). These
include MDS plots (analogues to PCA), detecting inefficient
immuno-precipitation or over-amplification artifacts, tools to
identify and test for genomic regions with large accumulation
of reads, and visualization of coverage profiles.

Oscar Reina

htSeqTools

Quality Control, Visualization and Processing for
High-Throughput Sequencing data

cmdsFit function

<dl> <dt><code>signature(d = "matrix")</code></dt><dd> Use Classical
  Multi-Dimensional Scaling to represent points 
  in a k-dimensional space.</dd> </dl>

Methods

Dimensionality of the reconstructed space, typically set to 2
  or 3.

Set to <code>"classic"</code> to perform classical MDS (uses
  function <code>cmdscale</code> from package <code>stats</code>). Set to
  <code>"isoMDS"</code> to use Kruskal's non-metric MDS (uses function
  <code>isoMDS</code> from package <code>MASS</code>).

Logical indicating if an additive constant c* should be
          computed, and added to the non-diagonal dissimilarities such
          that all n-1 eigenvalues are non-negative in <code>cmdscale</code>

A character string indicating which correlation
  coefficient (or covariance) is to be computed.  One of "pearson"
  (default), "kendall", or "spearman", can be abbreviated.

<code>cmdsFit</code> obtains coordinates in a <code>k</code> dimensional space
which best approximate the given distances between objects.

cmdsFit: Classical Multi-Dimensional Scaling for a distance matrix

Description

Usage

Arguments

Value

Methods

Examples