Class "RNAinteract"

Description

A class for double perturbation experiments (genetic interaction screens, drug-drug interaction screens). There are functions for creation, analysis, and display of interaction screens.

Objects from the Class

Objects can be created by calls of createRNAinteractFromFiles. See vignette("RNAinteract") for an example of creating an RNAinteract object.

Slots

data:

Object of class "array" with dimension sgi@F x sgi@S x sgi@C. The raw data of the screen.

screenNames:

Object of class "character" with length sgi@S.

channelNames:

Object of class "character" with length sgi@C.

well:

Object of class "character" with length sgi@F. Well name (e.g. F04) for each measurement.

plate:

Object of class "integer" with length sgi@F. Number of the plate for each measurement

pdim:

Object of class "integer" of length 2. Plate dimensions.

NT:

Object of class "integer" of length 1. Number of template reagents.

NQ:

Object of class "integer" of length 1. Number of query reagents.

C:

Object of class "integer" of length 1. Number of readout channels.

S:

Object of class "integer" of length 1. Number of screens.

F:

Object of class "integer" of length 1. Number of measurements or single experiments per screen.

reagents:

Object of class "data.frame" describing each reagents. Obligatory columns: RID and TID.

targets:

Object of class "data.frame" describing each target gene. Obligatory columns: TID, Symbol, group, GID.

templateDesign:

Object of class "data.frame" with sgi@NT rows describing the template design. Obligatory columns: TemplatePlate, Well, RID, QueryNr.

queryDesign:

Object of class "data.frame" with sgi@NQ rows describing the query design. Obligatory columns: Plate, TemplatePlate, QueryNr, RID.

transformation:

Object of class "character" of length sgi@C. The transformation applied to the input data.

mainTemplate:

Object of class "array" with dimension sgi@NT x sgi@S x sgi@C. The main effect of the template reagents.

mainQuery:

Object of class "array" with dimension sgi@NQ x sgi@S x sgi@C. The main effect of the query reagents.

mainSderrTemplate:

Object of class "array" with dimension sgi@NT x sgi@S x sgi@C. The standard error of the main effect of the template reagents.

mainSderrQuery:

Object of class "array" with dimension sgi@NQ x sgi@S x sgi@C. The standard error of the main effect of the query reagents.

mainSdTemplate:

Object of class "array" with dimension sgi@NQ x sgi@S x sgi@C. The standard deviation of the main effect of the query reagents.

mainSdQuery:

Object of class "array" with dimension sgi@NQ x sgi@S x sgi@C. The standard deviation of the main effect of the query reagents.

mainTimeEffect:

Object of class "array" with dimension sgi@NQ x sgi@S x sgi@C. The systematic changes of the query main effects, e.g. decreasing cell number over time.

mainSpatialEffect:

Object of class "array" with dimension sgi@F x sgi@S x sgi@C. The systematic spatial plate effects.

mainSpatialEffectRow:

Object of class "array". Spatial effects per row (as computed by Bscore).

mainSpatialEffectCol:

Object of class "array". Spatial effects per column (as computed by Bscore).

mainNeg:

Object of class "array" with dimension sgi@S x sgi@C. The main effect of the negative control.

mainNegTemplate:

Object of class "array" with dimension sgi@S x sgi@C. The template main effect of the negative control.

mainNegQuery:

Object of class "array" with dimension sgi@S x sgi@C. The query main effect of the negative control.

data2mainTemplate:

Object of class "integer" with dimension sgi@F. Mapping of single experiments to template reagents.

data2mainQuery:

Object of class "integer" with dimension sgi@F. Mapping of single experiments to query reagents.

ni.model:

Object of class "array" with dimension sgi@F x sgi@S x sgi@C. The expected values of the non-interacting model.

pi:

Object of class "array" with dimension sgi@F x sgi@S x sgi@C. The pairwise interaction score.

plateeffect:

Object of class "array".

p.value:

Object of class "array" with dimension sgi@NT x sgi@NQ x sgi@S x sgi@C describing the p.values.

q.value:

Object of class "array" with dimension sgi@NT x sgi@NQ x sgi@S x sgi@C describing the q.values.

Methods

show

signature(object = "RNAinteract"): ...

Author(s)

Bernd Fischer

See Also

RNAinteract-package

Examples

showClass("RNAinteract")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RNAinteract)
Loading required package: abind
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAinteract/RNAinteract-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: RNAinteract-class
> ### Title: Class "RNAinteract"
> ### Aliases: RNAinteract-class show,RNAinteract-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("RNAinteract")
Class "RNAinteract" [package "RNAinteract"]

Slots:
                                                                     
Name:                  data          screenNames         channelNames
Class:                array            character            character
                                                                     
Name:                  well                plate                 pdim
Class:            character              integer              integer
                                                                     
Name:                    NT                   NQ                    C
Class:              integer              integer              integer
                                                                     
Name:                     S                    F             reagents
Class:              integer              integer           data.frame
                                                                     
Name:               targets       templateDesign          queryDesign
Class:           data.frame           data.frame           data.frame
                                                                     
Name:        transformation         mainTemplate            mainQuery
Class:            character                array                array
                                                                     
Name:     mainSderrTemplate       mainSderrQuery       mainSdTemplate
Class:                array                array                array
                                                                     
Name:           mainSdQuery       mainTimeEffect    mainSpatialEffect
Class:                array                array                array
                                                                     
Name:  mainSpatialEffectRow mainSpatialEffectCol              mainNeg
Class:                array                array                array
                                                                     
Name:       mainNegTemplate         mainNegQuery    data2mainTemplate
Class:                array                array              integer
                                                                     
Name:        data2mainQuery             ni.model                   pi
Class:              integer                array                array
                                                                     
Name:           plateeffect              p.value              q.value
Class:                array                array                array
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>