Man pages for fCI
f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics

call.npcithe s4 class function
call.npci-methods~~ Methods for Function 'call.npci' ~~
computethe generic function 'compute' for s4 class
compute-methods~~ Methods for Function 'compute' ~~
deg.pairwise.fold.changefind targets that have a consistent fold change in the same...
deg.up.down.infofind targets and their detailed expression changes
deseq.median.ratio.normalizationdata matrix normalization method
divergence.multivariate.distributionsestimate fCI divergence for given samples of aritrary...
fCI.call.by.indextop level function call to find targets based on expression...
fCI-classClass '"fCI"'
fci.datadata frame of gene expression
figuresgeneric function to draw figures of the current analysis
figures-methodsgenerate figures for empirical null and case-control...
find.fci.targetsidentify differentially expressed genes
find.fci.targets-methods~~ Methods for Function 'find.fci.targets' ~~
find.mid.pointfind the middle value of the density distribution
get.fold.large.stepgenerate fold change cutoff values for fCI divergence...
get.npci.datareturn a fCI object given the gene expression data
get.npci.distance.matrixgenerate the divergence estimation based of fold change...
get.outline.indexfind the outline genes of a given distribution
get.protein.fold.stepgenerate fold-change cutoff on proteomics data (with large...
get.rank.combinationsfold change values
get.rna.fold.stepgenerate fCI fold-change cutoff values for typical RNA-Seq...
initialize-methods~~ Methods for Function 'initialize' ~~
intersect.of.listsfind the common values of all vectors of a list
is.installedpackage
multi.dimensional.fci.datadata frame of gene expression
normalizationgeneric function to normalize gene expression matrix
normalization-methods~~ Methods for Function 'normalization' ~~
NPCI-classClass '"NPCI"'
npci.gene.by.pvaluesfind most signficantly change fCI targets
npci.index.reconsideredfind targets that have little evidence to be differentially...
npci.index.to.be.removedgene indexes that will be considered as targets
npci.venn.diagramgenerate venn diagram for multiple fCI analysis
pairwise.change.occupancyfind the targets whose fold changes occur consistently...
populategeneric function to populate the fCI object based on provided...
populate-methods~~ Methods for Function 'populate' ~~
report.target.summarygenerate the results (gene ids) in the data frame
setfCIthe generic function 'setfCI' for s4 class
setfCI-methods~~ Methods for Function 'setfCI' ~~
show.targetsdisplay the gene ids that are identified to be differentially...
show.targets-methods~~ Methods for Function 'show.targets' ~~
summarizeresult summerization
summarize-methodsresult summerization
total.library.size.normalizationnormalize the gene expression based on the library size...
trim.size.normalizationnormalize gene expression by exluding genes on the top 5 and...
two.sample.log.ratiocompute the log ratios of two vectors
two.sample.permutation.testperform permuation test on two vectors
venndiagramgenerate a venn diagram to show the differentially expression...
venndiagram-methods~~ Methods for Function 'venndiagram' ~~
fCI documentation built on Nov. 17, 2017, 9:35 a.m.