NPCI-class              Class '"NPCI"'
call.npci               the s4 class function
call.npci-methods       ~~ Methods for Function 'call.npci' ~~
compute                 the generic function 'compute' for s4 class
compute-methods         ~~ Methods for Function 'compute' ~~
deg.pairwise.fold.change
                        find targets that have a consistent fold change
                        in the same direction (either up- or
                        down-regulation)
deg.up.down.info        find targets and their detailed expression
                        changes
deseq.median.ratio.normalization
                        data matrix normalization method
divergence.multivariate.distributions
                        estimate fCI divergence for given samples of
                        aritrary dimensions
fCI-class               Class '"fCI"'
fCI.call.by.index       top level function call to find targets based
                        on expression data and control & case indexes
fci.data                data frame of gene expression
figures                 generic function to draw figures of the current
                        analysis
figures-methods         generate figures for empirical null and
                        case-control distributions
find.fci.targets        identify differentially expressed genes
find.fci.targets-methods
                        ~~ Methods for Function 'find.fci.targets' ~~
find.mid.point          find the middle value of the density
                        distribution
get.fold.large.step     generate fold change cutoff values for fCI
                        divergence computation
get.npci.data           return a fCI object given the gene expression
                        data
get.npci.distance.matrix
                        generate the divergence estimation based of
                        fold change cutoff values
get.outline.index       find the outline genes of a given distribution
get.protein.fold.step   generate fold-change cutoff on proteomics data
                        (with large steps of 0.2-0.5 fold)
get.rank.combinations   fold change values
get.rna.fold.step       generate fCI fold-change cutoff values for
                        typical RNA-Seq data
initialize-methods      ~~ Methods for Function 'initialize' ~~
intersect.of.lists      find the common values of all vectors of a list
is.installed            package
multi.dimensional.fci.data
                        data frame of gene expression
normalization           generic function to normalize gene expression
                        matrix
normalization-methods   ~~ Methods for Function 'normalization' ~~
npci.gene.by.pvalues    find most signficantly change fCI targets
npci.index.reconsidered
                        find targets that have little evidence to be
                        differentially expressed
npci.index.to.be.removed
                        gene indexes that will be considered as targets
npci.venn.diagram       generate venn diagram for multiple fCI analysis
pairwise.change.occupancy
                        find the targets whose fold changes occur
                        consistently (upregulated or downregulated) in
                        all fCI analysis
populate                generic function to populate the fCI object
                        based on provided data
populate-methods        ~~ Methods for Function 'populate' ~~
report.target.summary   generate the results (gene ids) in the data
                        frame
setfCI                  the generic function 'setfCI' for s4 class
setfCI-methods          ~~ Methods for Function 'setfCI' ~~
show.targets            display the gene ids that are identified to be
                        differentially regulated
show.targets-methods    ~~ Methods for Function 'show.targets' ~~
summarize               result summerization
summarize-methods       result summerization
total.library.size.normalization
                        normalize the gene expression based on the
                        library size (summation) of the first sample
                        replicate
trim.size.normalization
                        normalize gene expression by exluding genes on
                        the top 5 and bottom 5 percentage
two.sample.log.ratio    compute the log ratios of two vectors
two.sample.permutation.test
                        perform permuation test on two vectors
venndiagram             generate a venn diagram to show the
                        differentially expression summaries accross
                        pairwise fCI analysis
venndiagram-methods     ~~ Methods for Function 'venndiagram' ~~
