Last data update: 2014.03.03

R: Estimated main effects
mainEffectsR Documentation

Estimated main effects

Description

Estimated main effects (single knock-down effects) for target and query genes. Additional overall effects for each phenotype are contained. The dataset contains an annotation of target genes, query genes, and phenotypes.

Usage

data(mainEffects)

Format

The format is: List of 4 $ target: num [1:289, 1:2, 1:2, 1:11, 1:2] -0.31065 -0.32253 -0.08466 -0.00367 -0.60867 ... ..- attr(*, "dimnames")=List of 5 .. ..$ targetGene : chr [1:289] "TDRD6" "PRDM11" "KDM1B" "INTS12" ... .. ..$ targetDesign: chr [1:2] "1" "2" .. ..$ 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" $ query : num [1:2, 1:20, 1:2, 1:11, 1:2] 0.277 0.265 0.235 0.226 1.165 ... ..- attr(*, "dimnames")=List of 5 .. ..$ 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" $ overall : num [1:2, 1:2, 1:11, 1:2] 0.3685 0.4638 0.3331 0.487 -0.0985 ... ..- attr(*, "dimnames")=List of 4 .. ..$ targetDesign: chr [1:2] "1" "2" .. ..$ 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(mainEffects, package="HD2013SGI")
print(dim(mainEffects$target))
plot(mainEffects$target[,1,1,1,1])

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/mainEffects.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mainEffects
> ### Title: Estimated main effects
> ### Aliases: mainEffects
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(mainEffects, package="HD2013SGI")
> print(dim(mainEffects$target))
[1] 289   2   2  11   2
> plot(mainEffects$target[,1,1,1,1])
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>