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.

Author
Shaojun Tang
Date of publication
None
Maintainer
Shaojun Tang <tangshao2008@gmail.com>
License
GPL (>= 2)
Version
1.4.0

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