Phenotypic data after quality control and feature selection

Description

Phenotypic features of pairwise genetic perturbation experiments after selection of non-redundant features and quality control. D is the 6-dimensional array of experimental measurements. Its dimensions are target genes x target siRNA designs x query genes x query siRNA designs x features x replicates. The array has a dimnames attribute, but there exists a more comprehensive annotation of target genes, query genes, and phenotypes in Anno.

Usage

data(datamatrix)

Format

The format is: List of 2 $ D : num [1:289, 1:2, 1:20, 1:2, 1:11, 1:2] -0.05334 -0.20294 -0.10123 0.33203 0.00638 ... ..- attr(*, "dimnames")=List of 6 .. ..$ targetGene : chr [1:289] "TDRD6" "PRDM11" "KDM1B" "INTS12" ... .. ..$ targetDesign: chr [1:2] "1" "2" .. ..$ queryGene : chr [1:20] "DPF2" "SMARCA1" "SMARCC1" "SMARCD2" ... .. ..$ queryDesign : chr [1:2] "1" "2" .. ..$ features : chr [1:11] "count" "cell.act.m.majoraxis" "nuc.nuc.b.q001" "nuc.0.m.eccentricity" ... .. ..$ replicate : chr [1:2] "1" "2" $ Anno:List of 3 ..$ target :'data.frame': 289 obs. of 4 variables: .. ..$ ID : chr [1:289] "B1" "B2" "B3" "B4" ... .. ..$ Symbol: chr [1:289] "TDRD6" "PRDM11" "KDM1B" "INTS12" ... .. ..$ Well : chr [1:289] "B1" "B2" "B3" "B4" ... .. ..$ group : chr [1:289] "sample" "sample" "sample" "sample" ... ..$ query :'data.frame': 20 obs. of 2 variables: .. ..$ ID : chr [1:20] "01" "02" "03" "04" ... .. ..$ Symbol: chr [1:20] "DPF2" "SMARCA1" "SMARCC1" "SMARCD2" ... ..$ phenotype: chr [1:11] "count" "cell.act.m.majoraxis" "nuc.nuc.b.q001" "nuc.0.m.eccentricity" ...

References

Laufer, Fischer et al., 2013

See Also

HD2013SGI

Examples

data(datamatrix, package="HD2013SGI")
plot(datamatrix$D[,1,1,1,1,1])

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(HD2013SGI)
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: geneplotter
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")'.

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

Loading required package: XML
Loading required package: splots
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

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

    plotMA

Loading required package: vcd
Loading required package: grid

Attaching package: 'vcd'

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

    tile

Loading required package: LSD
Loading required package: EBImage

Attaching package: 'EBImage'

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

    tile

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

    resize, tile

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

    channel

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/HD2013SGI/datamatrix.Rd_%03d_medium.png", width=480, height=480)
> ### Name: datamatrix
> ### Title: Phenotypic data after quality control and feature selection
> ### Aliases: datamatrix
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(datamatrix, package="HD2013SGI")
> plot(datamatrix$D[,1,1,1,1,1])
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>