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.

AuthorShaojun Tang
Date of publicationNone
MaintainerShaojun Tang <tangshao2008@gmail.com>
LicenseGPL (>= 2)
Version1.4.0

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' ~~

Files in this package

fCI/DESCRIPTION
fCI/NAMESPACE
fCI/R
fCI/R/buildfCI.R fCI/R/callfCI.R fCI/R/classfCI.R fCI/R/findDivergencefCI.R fCI/R/plotfCI.R fCI/R/postProcessfCI.R fCI/R/precomputefCI.R fCI/R/utils.R
fCI/build
fCI/build/vignette.rds
fCI/data
fCI/data/fci.RData
fCI/data/multi.dimensional.fci.RData
fCI/inst
fCI/inst/doc
fCI/inst/doc/fCI.R
fCI/inst/doc/fCI.Rmd
fCI/inst/doc/fCI.html
fCI/inst/extdata
fCI/inst/extdata/Fig1.png
fCI/inst/extdata/Fig2.png
fCI/inst/extdata/Fig3.png
fCI/inst/extdata/Formula.png
fCI/inst/extdata/Supp_Dataset_part_2.txt
fCI/inst/extdata/proteoGenomics.txt
fCI/man
fCI/man/NPCI-class.Rd fCI/man/call.npci-methods.Rd fCI/man/call.npci.Rd fCI/man/compute-methods.Rd fCI/man/compute.Rd fCI/man/deg.pairwise.fold.change.Rd fCI/man/deg.up.down.info.Rd fCI/man/deseq.median.ratio.normalization.Rd fCI/man/divergence.multivariate.distributions.Rd fCI/man/fCI-class.Rd fCI/man/fCI.call.by.index.Rd fCI/man/fci.data.Rd fCI/man/figures-methods.Rd fCI/man/figures.Rd fCI/man/find.fci.targets-methods.Rd fCI/man/find.fci.targets.Rd fCI/man/find.mid.point.Rd fCI/man/get.fold.large.step.Rd fCI/man/get.npci.data.Rd fCI/man/get.npci.distance.matrix.Rd fCI/man/get.outline.index.Rd fCI/man/get.protein.fold.step.Rd fCI/man/get.rank.combinations.Rd fCI/man/get.rna.fold.step.Rd fCI/man/initialize-methods.Rd fCI/man/intersect.of.lists.Rd fCI/man/is.installed.Rd fCI/man/multi.dimensional.fci.data.Rd fCI/man/normalization-methods.Rd fCI/man/normalization.Rd fCI/man/npci.gene.by.pvalues.Rd fCI/man/npci.index.reconsidered.Rd fCI/man/npci.index.to.be.removed.Rd fCI/man/npci.venn.diagram.Rd fCI/man/pairwise.change.occupancy.Rd fCI/man/populate-methods.Rd fCI/man/populate.Rd fCI/man/report.target.summary.Rd fCI/man/setfCI-methods.Rd fCI/man/setfCI.Rd fCI/man/show.targets-methods.Rd fCI/man/show.targets.Rd fCI/man/summarize-methods.Rd fCI/man/summarize.Rd fCI/man/total.library.size.normalization.Rd fCI/man/trim.size.normalization.Rd fCI/man/two.sample.log.ratio.Rd fCI/man/two.sample.permutation.test.Rd fCI/man/venndiagram-methods.Rd fCI/man/venndiagram.Rd
fCI/vignettes
fCI/vignettes/fCI.Rmd

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