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.