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Last data update: 2014.03.03

R: Interaction data generated by the analysis pipeline

interactions

R Documentation

Interaction data generated by the analysis pipeline

Description

This file contains the result of the analysis pipeline calling getInteractions.

Usage

data(interactions)

Format

List of 5
 $ anno  :List of 4
  ..$ drug:'data.frame':	1372 obs. of  15 variables
  ..$ line:'data.frame':	12 obs. of  4 variables
  ..$ repl: int [1:2]
  ..$ ftr : chr [1:20]
 $ D     : num [1:1372, 1:12, 1:2, 1:20]
 $ res   : num [1:1372, 1:12, 1:2, 1:20]
 $ effect:List of 2
  ..$ drug: num [1:1372, 1:2, 1:20]
  ..$ line: num [1:12, 1:2, 1:20]
 $ pVal  : num [1:1372, 1:12, 1:20, 1:3]

Value

interactions is a list containing the list anno, array D, array res, list effect and array pVal.

The annotation anno is represented as a list containing a data.frame drug with the drug annotation, a data.frame line with the cell line annotation, a vector repl with the information about the replicates and a vector ftr with the feature names.

The four dimensional array D contains the glog transformed feature data of the features selected for the final analysis. The dimensions represent:

drug
cell line
replicate
feature

The four dimensional array res contains the interaction terms. It has the same dimentions as D. The dimensions represent:

drug
cell line
replicate
feature

The list effect contains the drug and cell line effect as three-dimensional array: drug and line have the following dimensions:

drug or cell line respectively
replicate
feature

pVal is an array containing the p-values, adjusted p-values and correlation between replicates of interactions. The dimensions represent:

drug
cell line
p-value, adjusted p-value, correlation
feature

Examples

data(interactions)
str(interactions)

Results


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> library(PGPC)
Loading required package: EBImage
Loading required package: imageHTS
Loading required package: cellHTS2
Loading required package: RColorBrewer
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")'.


Attaching package: 'Biobase'

The following object is masked from 'package:EBImage':

    channel

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: grid
Loading required package: SearchTrees
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: ggplot2

Attaching package: 'ggplot2'

The following object is masked from 'package:cellHTS2':

    annotate

Loading required package: geneplotter
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:gplots':

    space

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

    colMeans, colSums, expand.grid, rowMeans, rowSums


Attaching package: 'IRanges'

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

    resize, tile

Loading required package: XML
Loading required package: ChemmineR

Attaching package: 'ChemmineR'

The following object is masked from 'package:S4Vectors':

    fold

The following object is masked from 'package:limma':

    makeUnique

Loading required package: reshape2
Loading required package: plyr

Attaching package: 'plyr'

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PGPC/interactions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: interactions
> ### Title: Interaction data generated by the analysis pipeline
> ### Aliases: interactions
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(interactions)
> str(interactions)
List of 5
 $ anno  :List of 4
  ..$ drug:'data.frame':	1372 obs. of  15 variables:
  .. ..$ PlateName           : chr [1:1372] "P1" "P1" "P1" "P1" ...
  .. ..$ Well                : chr [1:1372] "A03" "A04" "A05" "A06" ...
  .. ..$ Content             : chr [1:1372] "sample" "sample" "sample" "sample" ...
  .. ..$ compoundID_384      : chr [1:1372] "78875" "78955" "78876" "78956" ...
  .. ..$ compoundID          : chr [1:1372] "78875" "78955" "78876" "78956" ...
  .. ..$ mol.weight.Structure: chr [1:1372] "195,22001" "163,19638" "202,25818" "131,17601" ...
  .. ..$ Name                : chr [1:1372] "DL-alpha-Methyl-p-tyrosine" "N-Acetyl-L-Cysteine" "6-Methoxy-1,2,3,4-tetrahydro-9H-pyrido[3,4b] indole" "6-Aminohexanoic acid" ...
  .. ..$ SecName             : chr [1:1372] "4-Hydroxy-alpha-methylphenylalanine" "" "" "6-Aminocaproic acid; EACA" ...
  .. ..$ Class               : chr [1:1372] "Neurotransmission" "Glutamate" "Neurotransmission" "Immune System" ...
  .. ..$ Enzyme              : chr [1:1372] "Enzyme" "" "Enzyme" "" ...
  .. ..$ Action              : chr [1:1372] "Inhibitor" "Antagonist" "Inhibitor" "Inhibitor" ...
  .. ..$ Selectivity         : chr [1:1372] "Tyrosine hydroxylase" "" "MAO" "Blood Clotting" ...
  .. ..$ Description         : chr [1:1372] "Inhibitor of catecholamine synthesis and tyrosine hydroxylase" "Amino acid analog that partially improves neuronal survival following transient forebrain ischemia" "MAO inhibitor" "Promotes rapid dissociation of plasmin, thereby inhibiting the activation of plasminogen and subsequent fibrinolysis; inhibits "| __truncated__ ...
  .. ..$ GeneID              : chr [1:1372] "78875" "78955" "78876" "78956" ...
  .. ..$ Selectivity_updated : chr [1:1372] "Tyrosine hydroxylase" "AA-analog" "MAO" "Blood Clotting" ...
  ..$ line:'data.frame':	12 obs. of  4 variables:
  .. ..$ name            : chr [1:12] "02-006" "02-031" "02-004" "104-009" ...
  .. ..$ mutationDetailed: chr [1:12] "AKT1-/-&AKT2-/-" "MEK2-/-" "AKT1-/-" "CTNNB1 mt-/wt+" ...
  .. ..$ mutation        : chr [1:12] "AKT1/2" "MEK2" "AKT1" "CTNNB1 wt" ...
  .. ..$ startPlate      : num [1:12] 1 5 9 13 17 21 25 29 33 37 ...
  ..$ repl: int [1:2] 1 2
  ..$ ftr : chr [1:20] "n" "cseg.act.m.majoraxis.mean" "cseg.act.h.cor.s1.mean" "nseg.0.m.majoraxis.mean" ...
 $ D     : num [1:1372, 1:12, 1:2, 1:20] 0.871 0.937 0.867 0.963 0.936 ...
 $ res   : num [1:1372, 1:12, 1:2, 1:20] -0.04 -0.0445 -0.0237 0.0457 0.0094 ...
 $ effect:List of 2
  ..$ drug: num [1:1372, 1:2, 1:20] -0.07399 -0.00358 -0.09446 -0.06819 -0.05889 ...
  ..$ line: num [1:12, 1:2, 1:20] 0.00308 0.00912 0.02849 -0.03774 0.01623 ...
 $ pVal  : num [1:1372, 1:12, 1:20, 1:3] 0.3147 0.2682 0.3243 0.9013 0.0763 ...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>