fCI-class: Class '"fCI"'

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

Description

The main Class that defines the slots values

Objects from the Class

Objects can be created by calls of the form new("fCI", ...).

Slots

sample.data.file:

Object of class "character" ~~

distance.matrix:

Object of class "matrix" ~~

sample.data.normalized:

Object of class "data.frame" ~~

attr.info:

Object of class "data.frame" ~~

null.data.start:

Object of class "matrix" ~~

diff.data.start:

Object of class "matrix" ~~

expr.by.fold:

Object of class "matrix" ~~

fold.cutoff.list:

Object of class "list" ~~

rank.index.to.be.removed:

Object of class "list" ~~

diff.gene.ids:

Object of class "list" ~~

wt.index:

Object of class "numeric" ~~

df.index:

Object of class "numeric" ~~

ctr.indexes:

Object of class "numeric" ~~

trt.indexes:

Object of class "numeric" ~~

method.option:

Object of class "numeric" ~~

use.ratio:

Object of class "logical" ~~

percent.genes.to.scan:

Object of class "numeric" ~~

num.genes.to.skip.each:

Object of class "numeric" ~~

use.fold.change:

Object of class "logical" ~~

wt.comb:

Object of class "list" ~~

df.comb:

Object of class "list" ~~

diff.ids:

Object of class "list" ~~

result:

Object of class "numeric" ~~

indexes.reconsidered:

Object of class "numeric" ~~

center.by.gaussian.kernel:

Object of class "logical" ~~

symmetric.fold:

Object of class "logical" ~~

pairwise.diff.gene.ids:

Object of class "list" ~~

Methods

No methods defined with class "fCI" in the signature.

Note

TBD

Author(s)

Shaojun Tang

References

http://software.steenlab.org/fCI/

See Also

TBD

Examples

showClass("fCI")

Example output

sh: 1: cannot create /dev/null: Permission denied
Loading required package: FNN
Loading required package: psych
Loading required package: gtools

Attaching package: ‘gtools’

The following object is masked from ‘package:psych’:

    logit

Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

Loading required package: rgl
Loading required package: grid
Loading required package: VennDiagram
Loading required package: futile.logger

Attaching package: ‘futile.logger’

The following object is masked from ‘package:gtools’:

    scat

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. 
Class "fCI" [package "fCI"]

Slots:
                                                          
Name:           sample.data.file           distance.matrix
Class:                 character                    matrix
                                                          
Name:     sample.data.normalized                 attr.info
Class:                data.frame                data.frame
                                                          
Name:            null.data.start           diff.data.start
Class:                    matrix                    matrix
                                                          
Name:               expr.by.fold          fold.cutoff.list
Class:                    matrix                      list
                                                          
Name:   rank.index.to.be.removed             diff.gene.ids
Class:                      list                      list
                                                          
Name:                   wt.index                  df.index
Class:                   numeric                   numeric
                                                          
Name:                ctr.indexes               trt.indexes
Class:                   numeric                   numeric
                                                          
Name:              method.option                 use.ratio
Class:                   numeric                   logical
                                                          
Name:      percent.genes.to.scan    num.genes.to.skip.each
Class:                   numeric                   numeric
                                                          
Name:            use.fold.change                   wt.comb
Class:                   logical                      list
                                                          
Name:                    df.comb                  diff.ids
Class:                      list                      list
                                                          
Name:                     result      indexes.reconsidered
Class:                   numeric                   numeric
                                                          
Name:  center.by.gaussian.kernel            symmetric.fold
Class:                   logical                   logical
                                
Name:     pairwise.diff.gene.ids
Class:                      list

fCI documentation built on Nov. 8, 2020, 6:53 p.m.