BaseIndexList-class     An S4 class to hold a list of indices, with the
                        possibility to specify the offset of the
                        indices. IndexList and SignedIndexList extend
                        this class
GmtList                 Convert a list to a GmtList object
GmtList-class           An S4 class to hold geneset in the GMT file in
                        a list, each item in the list is in in turn a
                        list containing following items: name, desc,
                        and genes.
IndexList               Convert a list to an IndexList object
IndexList-class         An S4 class to hold a list of integers as
                        indices, with the possibility to specify the
                        offset of the indices
SignedGenesets          Convert a list to a SignedGenesets object
SignedGenesets-class    An S4 class to hold signed genesets, each item
                        in the list is in in turn a list containing
                        following items: name, pos, and neg.
SignedIndexList         Convert a list into a SignedIndexList
SignedIndexList-class   An S4 class to hold a list of signed integers
                        as indices, with the possibility to specify the
                        offset of the indices
absLog10p               Absolute base-10 logarithm of p-values
as.gmtlist              Convert a list of gene symbols into a gmtlist
entropy                 Shannon entropy and related concepts
filterPmat              Filter rows of p-value matrix under the
                        significance threshold
gini                    Calculate Gini Index of a numeric vector
gmtlist2signedGenesets
                        Convert gmtlist into a list of signed genesets
matchGenes              Match genes in a list-like object to a vector
                        of genesymbols
offset,BaseIndexList-method
                        Get offset from an IndexList object
offset<-                Set the offset of an 'IndexList' or a
                        'SignedIndexList' object
readGmt                 Read in gene sets from a GMT file
readSignedGmt           Read signed GMT files
simplifyMatrix          Simplify matrix in case of single row/columns
valTypes                prints the options of valTypes of wmwTest
wmwTest                 Wilcoxon-Mann-Whitney rank sum test for
                        high-throughput expression profiling data
wmwTestInR              Wilcoxon-Mann-Whitney test in R
