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

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' ~~ |

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