Changes in version 1.8.0
o
New function MDtest is introduced. It implements a
nonparametric multivariate test of means based on sample
ranking in the MST similar to function KStest, but the test
statistic is the mean deviation between the CDFs of two
conditions.
o
New function RMDtest is introduced. It implements a
nonparametric multivariate test of variance based on sample
ranking in the MST similar to function RKStest, but the test
statistic is the mean deviation between the CDFs of two
conditions.
o
New function AggrFtest is introduced. It implements a
nonparametric test of variance by aggregating the univariate
p-values obtained by the F-test using Fisher's probability
combining method. It test the hypothesis that all genes in a
gene set show no significant difference in variance between two
conditions against the alternative hypothesis that at least one
gene in the gene set shows significant difference in variance
between two conditions.
o
New function findMST2.PPI is introduced. It finds the union of
the first and second MSTs similar to function findMST2, but it
accepts an object of class igraph as input rather that a matrix
of gene expression data. The input igraph object represents a
protein-protein interaction (PPI) network that can be binary or
weighted, directed or undirected.
o
New wrapper function TestGeneSets is introduced. It performs a
specific statistical method from the ones available in package
GSAR for multiple gene sets. The gene sets are provided as a
list of character vectors where each entry has the feature
(gene) identifiers in a single gene set.
o
New argument pvalue.only added to all available statistical
methods in the package. When pvalue.only=TRUE (default), each
statistical method returns the p-value only. When
pvalue.only=FALSE, each statistical method returns a list of
length 3 consisting of the observed statistic, vector of
permuted statistics, and p-value.
o
New arguments leg.x, leg.y, group1.name, group2.name,
label.color, label.dist, vertex.size, vertex.label.font, and
edge.width added to function plotMST2.pathway to allow more
flexibility in generating plots. The values of most of these
arguments are passed to function plot.igraph.
Changes in version 1.4.0
o
New argument return.weights added to function plotMST2.pathway.
If return.weights=TRUE, the weight vectors found by GSNCA for
the genes under two classes are returned as a 2-column matrix.
Changes in version 1.2.2
o
Bug fix in function HDP.ranking to accomodate the changes in
package igraph (version 1.0.1).
o
Additional steps added to the code of the second case study in
the vignette to filter C2 gene sets properly.
o
Minor changes in the vignette.
Changes in version 1.0.0
o
The package provides two-sample nonparametric multivariate
statistical methods to test specific alternative hypotheses
against a null hypothesis.
o
GSAR depends on package igraph to handle graphs in objects of
class igraph and uses some functions too.
o
New capabilities and future changes will be reported in
subsequent versions.