RKStest: Multivariate Radial Kolmogorov-Smirnov Test of Variance

In GSAR: Gene Set Analysis in R

Description

Performs two-sample nonparametric multivariate test of variance based on the minimum spanning tree (MST) and Kolmogorov-Smirnov statistic. It tests the null hypothesis that a set of features has the same scale in two conditions versus different scales.

Usage

RKStest(object, group, mst.order=1, nperm=1000, pvalue.only=TRUE)

Arguments

object	a numeric matrix with columns and rows respectively corresponding to samples and features.
group	a numeric vector indicating group associations for samples. Possible values are 1 and 2.
mst.order	numeric value to indicate the consideration of the union of the first mst.order MSTs. Default value is 1. Maximum allowed value is 5.
nperm	number of permutations used to estimate the null distribution of the test statistic. If not given, a default value 1000 is used.
pvalue.only	logical. If TRUE (default), the p-value is returned. If FALSE a list of length three containing the observed statistic, the vector of permuted statistics, and the p-value is returned.

Details

This function tests the null hypothesis that a set of features has the same scale in two conditions. It performs a two-sample nonparametric multivariate test based on the minimum spanning tree (MST) and Kolmogorov-Smirnov statistic as proposed by Friedman and Rafsky (1979). The MST of the weighted undirectional graph created from the samples is found. The nodes of the MST are ranked based on their position in the MST. The MST is rooted at the node with smallest geodisic distance (rank 1) and nodes with higher depths from the root are assigned higher ranks. The quantity d_i = (r_i / n_1) - (s_i / n_2) is calculated where r_i(s_i) is the number of nodes (samples) from condition 1(2) which ranked lower than i, 1 ≤ i ≤ N and N is the total number of samples. The Kolmogorov-Smirnov statistic is given by the maximum absolute difference D = √{\frac{n_{1}n_{2}}{n_{1}+n_{2}}} max|d_i|. The performance of this test under different alternative hypotheses was thoroughly examind in Rahmatallah et. al. (2012). The null distribution of the test statistic is estimated by permuting sample labels nperm times and calculating the test statistic for each. P-value is calculated as

p.value = \frac{∑_{k=1}^{nperm} I ≤ft[ D_{k} ≥q D_{obs} \right] + 1}{nperm + 1}

where D_{k} is the test statistic for permutation k, D_{obs} is the observed test statistic, and I is the indicator function.

Value

When pvalue.only=TRUE (default), function RKStest returns the p-value indicating the attained significance level. When pvalue.only=FALSE, function RKStest produces a list of length 3 with the following components:

statistic	the value of the observed test statistic.
perm.stat	numeric vector of the resulting test statistic for nperm random permutations of sample labels.
p.value	p-value indicating the attained significance level.

Note

The variance of both the Poisson and negative Bionomial distributions, used to model count data, is a function of their mean. Therefore, using the radial Kolmogorov-Smirnov test (RKStest) to detect pathways with differential variance for RNA-Seq counts is not recommended without proper data normalization.

Author(s)

Yasir Rahmatallah and Galina Glazko

References

Rahmatallah Y., Emmert-Streib F. and Glazko G. (2012) Gene set analysis for self-contained tests: complex null and specific alternative hypotheses. Bioinformatics 28, 3073–3080.

Friedman J. and Rafsky L. (1979) Multivariate generalization of the Wald-Wolfowitz and Smirnov two-sample tests. Ann. Stat. 7, 697–717.

See Also

RMDtest, WWtest, MDtest, KStest.

Examples

## generate a feature set of length 20 in two conditions
## each condition has 20 samples
## use multivariate normal distribution
library(MASS)
ngenes <- 20
nsamples <- 40
## let the mean vector have zeros of length 20 for both conditions
zero_vector <- array(0,c(1,ngenes))
## set the covariance matrix to be an identity matrix for condition 1
cov_mtrx <- diag(ngenes)
gp1 <- mvrnorm((nsamples/2), zero_vector, cov_mtrx)
## set some scale difference in the covariance matrix for condition 2
cov_mtrx <- cov_mtrx*3
gp2 <- mvrnorm((nsamples/2), zero_vector, cov_mtrx)
## combine the data of two conditions into one dataset
gp <- rbind(gp1,gp2)
dataset <- aperm(gp, c(2,1))
## first 20 samples belong to group 1
## second 20 samples belong to group 2
pvalue <- RKStest(object=dataset, group=c(rep(1,20),rep(2,20)))

Example output

Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

GSAR documentation built on Nov. 8, 2020, 7:16 p.m.