fCI: f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics
Version 1.6.0

(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
Bioconductor views Proteomics
Date of publicationNone
MaintainerShaojun Tang <tangshao2008@gmail.com>
LicenseGPL (>= 2)
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("fCI")

Getting started

fCI"

Popular man pages

compute: the generic function 'compute' for s4 class
fci.data: data frame of gene expression
figures: generic function to draw figures of the current analysis
get.rna.fold.step: generate fCI fold-change cutoff values for typical RNA-Seq...
intersect.of.lists: find the common values of all vectors of a list
normalization-methods: ~~ Methods for Function 'normalization' ~~
npci.venn.diagram: generate venn diagram for multiple fCI analysis
See all...

All man pages Function index File listing

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' ~~

Functions

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

Files

DESCRIPTION
NAMESPACE
R
R/buildfCI.R
R/callfCI.R
R/classfCI.R
R/findDivergencefCI.R
R/plotfCI.R
R/postProcessfCI.R
R/precomputefCI.R
R/utils.R
build
build/vignette.rds
data
data/fci.RData
data/multi.dimensional.fci.RData
inst
inst/doc
inst/doc/fCI.R
inst/doc/fCI.Rmd
inst/doc/fCI.html
inst/extdata
inst/extdata/Fig1.png
inst/extdata/Fig2.png
inst/extdata/Fig3.png
inst/extdata/Formula.png
inst/extdata/Supp_Dataset_part_2.txt
inst/extdata/proteoGenomics.txt
man
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
vignettes
vignettes/fCI.Rmd
fCI documentation built on May 20, 2017, 9:26 p.m.

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