# f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics

## Documentation for package ‘fCI’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

call.npci | the s4 class function
call.npci-method | ~~ Methods for Function 'call.npci' ~~
call.npci-methods | ~~ Methods for Function 'call.npci' ~~
compute | the generic function 'compute' for s4 class
compute-method | ~~ Methods for Function 'compute' ~~
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-method | generate figures for empirical null and case-control distributions
figures-methods | generate figures for empirical null and case-control distributions
find.fci.targets | identify differentially expressed genes
find.fci.targets-method | ~~ Methods for Function 'find.fci.targets' ~~
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-method | ~~ Methods for Function 'initialize' ~~
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-method | ~~ Methods for Function 'normalization' ~~
normalization-methods | ~~ Methods for Function 'normalization' ~~
NPCI-class | Class '"NPCI"'
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-method | ~~ Methods for Function 'populate' ~~
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-method | ~~ Methods for Function 'setfCI' ~~
setfCI-methods | ~~ Methods for Function 'setfCI' ~~
show.targets | display the gene ids that are identified to be differentially regulated
show.targets-method | ~~ Methods for Function 'show.targets' ~~
show.targets-methods | ~~ Methods for Function 'show.targets' ~~
summarize | result summerization
summarize-method | 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-method | ~~ Methods for Function 'venndiagram' ~~
venndiagram-methods | ~~ Methods for Function 'venndiagram' ~~