kimod (version 1.0.0)

GroupProj: GroupProj of SelectVar object

Description

This function calculates the relashionship between genes and samples from SelectVar method. Also, computes agglomerative hierarchical clustering of the dataset.

Usage

GroupProj(object, NGroups = 2, metric = c("euclidean", "manhattan"),
  method = c("ward", "single", "complete", "weighted", "flexible"), ...)

## S3 method for class 'SelectVar':
GroupProj(object, NGroups = 2, metric = c("euclidean",
  "manhattan"), method = c("ward", "single", "complete", "weighted",
  "flexible"), ...)

Arguments

object

it is an object of SelectVar Class.

NGroups

An integer scalar or vector with the desired number of clusters.

metric

The character string specifying the metric to be used to calculate dissimilarities between observations. The currently available options are "euclidean" and "manhattan". Euclidean distances are root sum-of-squares of differences, and manhattan distances are the sum of absolute differences.

method

character string defining the clustering method. The methods implemented are "average" ([unweighted pair-] group [arithMetic] average method, aka b "single" (single linkage), "complete" (complete linkage), "ward" (Ward's method), "weighted" (weighted average linkage, aka b its generalization "flexible" which uses (a constant version of) the Lance-Williams formula and the par.method argument, and "gaverage" a generalized "average" aka b also using the Lance-Williams formula and par.method. (See agnes).

...

Additional parameters for agnes.

Value

• GroupProj
  GroupProj with the corresponding completed slots

Examples

{
data(NCI60Selec)
Z1<-DiStatis(NCI60Selec)
M1<-SelectVar(Z1,Crit="R2-Adj")
A1<-GroupProj(M1,method="ward",metric="euclidean",NGroups=6)
data(winesassesors)
Z2<-DiStatis(winesassesors)
M2<-SelectVar(Z2,Crit="R2-Adj")
A2<-GroupProj(M2,method="ward",metric="euclidean",NGroups=6)
}