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

(f-divergence Cutoff Index), is to find DEGs in the transcriptomic & proteomic data, and identify DEGs by computing the difference between the distribution of fold-changes for the control-control and remaining (non-differential) case-control gene expression ratio data. fCI provides several advantages compared to existing methods.

Install the latest version of this package by entering the following in R:
AuthorShaojun Tang
Bioconductor views Proteomics
Date of publicationNone
MaintainerShaojun Tang <tangshao2008@gmail.com>
LicenseGPL (>= 2)

View on Bioconductor

Man pages

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...

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...

fCI.call.by.index: top level function call to find targets based on expression...

fCI-class: Class '"fCI"'

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...

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...

get.npci.data: return a fCI object given the gene expression data

get.npci.distance.matrix: generate the divergence estimation based of fold change...

get.outline.index: find the outline genes of a given distribution

get.protein.fold.step: generate fold-change cutoff on proteomics data (with large...

get.rank.combinations: fold change values

get.rna.fold.step: generate fCI fold-change cutoff values for typical RNA-Seq...

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-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...

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...

populate: generic function to populate the fCI object based on provided...

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...

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...

trim.size.normalization: normalize gene expression by exluding genes on the top 5 and...

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...

venndiagram-methods: ~~ Methods for Function 'venndiagram' ~~


call.npci Man page
call.npci-methods Man page
call.npci,NPCI-method Man page
compute Man page
compute-methods Man page
compute,NPCI-method Man page
deg.pairwise.fold.change Man page
deg.up.down.info Man page
deseq.median.ratio.normalization Man page
divergence.multivariate.distributions Man page
fCI.call.by.index Man page
fCI-class Man page
fci.data Man page
figures Man page
figures-methods Man page
figures,NPCI-method Man page
find.fci.targets Man page
find.fci.targets-methods Man page
find.fci.targets,NPCI-method Man page
find.mid.point Man page
get.fold.large.step Man page
get.npci.data Man page
get.npci.distance.matrix Man page
get.outline.index Man page
get.protein.fold.step Man page
get.rank.combinations Man page
get.rna.fold.step Man page
initialize-methods Man page
initialize,NPCI-method Man page
intersect.of.lists Man page
is.installed Man page
multi.dimensional.fci.data Man page
normalization Man page
normalization-methods Man page
normalization,NPCI-method Man page
NPCI-class Man page
npci.gene.by.pvalues Man page
npci.index.reconsidered Man page
npci.index.to.be.removed Man page
npci.venn.diagram Man page
pairwise.change.occupancy Man page
populate Man page
populate-methods Man page
populate,NPCI-method Man page
report.target.summary Man page
setfCI Man page
setfCI-methods Man page
setfCI,NPCI-method Man page
show.targets Man page
show.targets-methods Man page
show.targets,NPCI-method Man page
summarize Man page
summarize-methods Man page
summarize,NPCI-method Man page
total.library.size.normalization Man page
trim.size.normalization Man page
two.sample.log.ratio Man page
two.sample.permutation.test Man page
venndiagram Man page
venndiagram-methods Man page
venndiagram,NPCI-method Man page


R/buildfCI.R R/callfCI.R R/classfCI.R R/findDivergencefCI.R R/plotfCI.R R/postProcessfCI.R R/precomputefCI.R R/utils.R
man/NPCI-class.Rd man/call.npci-methods.Rd man/call.npci.Rd man/compute-methods.Rd man/compute.Rd man/deg.pairwise.fold.change.Rd man/deg.up.down.info.Rd man/deseq.median.ratio.normalization.Rd man/divergence.multivariate.distributions.Rd man/fCI-class.Rd man/fCI.call.by.index.Rd man/fci.data.Rd man/figures-methods.Rd man/figures.Rd man/find.fci.targets-methods.Rd man/find.fci.targets.Rd man/find.mid.point.Rd man/get.fold.large.step.Rd man/get.npci.data.Rd man/get.npci.distance.matrix.Rd man/get.outline.index.Rd man/get.protein.fold.step.Rd man/get.rank.combinations.Rd man/get.rna.fold.step.Rd man/initialize-methods.Rd man/intersect.of.lists.Rd man/is.installed.Rd man/multi.dimensional.fci.data.Rd man/normalization-methods.Rd man/normalization.Rd man/npci.gene.by.pvalues.Rd man/npci.index.reconsidered.Rd man/npci.index.to.be.removed.Rd man/npci.venn.diagram.Rd man/pairwise.change.occupancy.Rd man/populate-methods.Rd man/populate.Rd man/report.target.summary.Rd man/setfCI-methods.Rd man/setfCI.Rd man/show.targets-methods.Rd man/show.targets.Rd man/summarize-methods.Rd man/summarize.Rd man/total.library.size.normalization.Rd man/trim.size.normalization.Rd man/two.sample.log.ratio.Rd man/two.sample.permutation.test.Rd man/venndiagram-methods.Rd man/venndiagram.Rd

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