testOneConnectedComponent: Applies a series of two-sample tests to a connected graph...

In DEGraph: Two-sample tests on a graph

Description

Applies a series of two-sample tests to a connected graph using various statistics.

Usage

testOneConnectedComponent(graph, data, classes, ..., prop=0.2, verbose=FALSE)

Arguments

graph	A graph object.
data	A 'numeric matrix (size: number 'p' of genes x number 'n' of samples) of gene expression.
classes	A character vector (length: 'n') of class assignments.
...	Further arguments to be passed to laplacianFromA().
prop	A numeric value, percentage of components retained for Fourier and PCA.
verbose	If TRUE, extra information is output.

Details

This function performs the test, assuming that all genes in the graph are represented in the expression data set, in order not to have to modify the graph topology.

Interaction signs are used if available in the graph ('getSignedGraph' is not called here, in order not to have to modify the graph topology.).

The graph given as input has to have only one connex component. It can be retrieved from the output of getConnectedComponentList().

Value

A structured list containing the p-values of the tests, the graph object of the connected component and the number of retained Fourier dimensions.

Author(s)

Laurent Jacob, Pierre Neuvial and Sandrine Dudoit

See Also

testOneGraph() getConnectedComponentList()

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.