f-divergence Cutoff Index


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Documentation for package ‘fCI’ version 1.0.0

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call.npci the s4 class function
call.npci-method ~~ Methods for Function 'call.npci' ~~
call.npci-methods ~~ Methods for Function 'call.npci' ~~
compute the generic function 'compute' for s4 class
compute-method ~~ Methods for Function 'compute' ~~
compute-methods ~~ Methods for Function 'compute' ~~
deg.pairwise.fold.change find targets that have a consistent fold change in the same direction (either up- or down-regulation)
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 dimensions
fCI-class Class '"fCI"'
fCI.call.by.index top level function call to find targets based on expression data and control & case indexes
fci.data data frame of gene expression
figures generic function to draw figures of the current analysis
figures-method generate figures for empirical null and case-control distributions
figures-methods generate figures for empirical null and case-control distributions
find.fci.targets identify differentially expressed genes
find.mid.point find the middle value of the density distribution
get.fold.large.step generate fold change cutoff values for fCI divergence computation
get.npci.data return a fCI object given the gene expression data
get.npci.distance.matrix generate the divergence estimation based of fold change cutoff values
get.outline.index find the outline genes of a given distribution
get.protein.fold.step generate fold-change cutoff on proteomics data (with large steps of 0.2-0.5 fold)
get.rank.combinations fold change values
get.rna.fold.step generate fCI fold-change cutoff values for typical RNA-Seq data
initialize-method ~~ Methods for Function 'initialize' ~~
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-method ~~ Methods for Function 'normalization' ~~
normalization-methods ~~ Methods for Function 'normalization' ~~
npci.gene.by.pvalues find most signficantly change fCI targets
npci.index.reconsidered find targets that have little evidence to be differentially expressed
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 (upregulated or downregulated) in all fCI analysis
populate generic function to populate the fCI object based on provided data
populate-method ~~ Methods for Function 'populate' ~~
populate-methods ~~ Methods for Function 'populate' ~~
report.target.summary generate the results (gene ids) in the data frame
show.targets display the gene ids that are identified to be differentially regulated
summarize result summerization
summarize-method result summerization
summarize-methods result summerization
total.library.size.normalization normalize the gene expression based on the library size (summation) of the first sample replicate
trim.size.normalization normalize gene expression by exluding genes on the top 5 and bottom 5 percentage
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 summaries accross pairwise fCI analysis
venndiagram-method ~~ Methods for Function 'venndiagram' ~~
venndiagram-methods ~~ Methods for Function 'venndiagram' ~~