graph.T2.test: Performs the Hotelling T2 test in Fourier space

In DEGraph: Two-sample tests on a graph

Description

Performs the Hotelling T2 test in Fourier space.

Usage

graph.T2.test(X1, X2, G=NULL, lfA=NULL, ..., k=ncol(X1))

Arguments

X1	A n1 x p numeric matrix, observed data for class 1: p variables, n1 observations.
X2	A n2 x p numeric matrix, observed data for class 2: p variables, n2 observations.
G	An object of class graphAM or graphNEL, the graph to be used in the two-sample test.
lfA	A list returned by laplacianFromA(), containing the Laplacian eigen vectors and eigen values
...	Further arguments to be passed to laplacianFromA().
k	A numeric value, number of Fourier components retained for the test.

Value

A list with class "htest", as returned by T2.test.

Author(s)

Laurent Jacob, Pierre Neuvial and Sandrine Dudoit

See Also

T2.test graphAM

Examples

library("rrcov")

## Some parameters
n1 <- n2 <- 20
nnodes <- nedges <- 20
k <- 3
ncp <- 0.5
sigma <- diag(nnodes)/sqrt(nnodes)


## Build graph, decompose laplacian
G <- randomWAMGraph(nnodes=nnodes,nedges=nedges)
A <- G@adjMat
lfA <- laplacianFromA(A,ltype="unnormalized")
U <- lfA$U
l <- lfA$l

## Build two samples with smooth mean shift
X <- twoSampleFromGraph(n1,n2,shiftM2=ncp,sigma,U=U,k=k)

## Do hypothesis testing
t <- T2.test(X$X1,X$X2) # Raw T-square
print(t$p.value)
tu <- graph.T2.test(X$X1,X$X2,lfA=lfA,k=k) # Filtered T-squares
print(tu$p.value)

Example output

Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following objects are masked from 'package:methods':

    getClasses, getMethods

The following objects are masked from 'package:base':

    attach, detach, gc, load, save

R.utils v2.8.0 successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

The following object is masked from 'package:utils':

    timestamp

The following objects are masked from 'package:base':

    cat, commandArgs, getOption, inherits, isOpen, parse, warnings

Loading required package: robustbase
Scalable Robust Estimators with High Breakdown Point (version 1.4-7)


Attaching package: 'rrcov'

The following object is masked from 'package:R.utils':

    getRaw

Warning message:
In sqrt(shiftM2) * diff[1:k]/sqrt(rawShiftNorm) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

[1] 0.1850897
[1] 0.0001517197

DEGraph documentation built on Nov. 8, 2020, 5:52 p.m.