The genetic interaction data.

Description

The genetic interaction data. Pairwise interaction scores (piscore) are presented in a 6-dimensional array with dimensions target genes x target siRNA designs x query genes x query siRNA designs x features x replicates. BH-corrected p-values (padj) are presented in a 5-dimensional array with dimensions target genes x target siRNA designs x query genes x query siRNA designs x features. An annotation of target and query genes and of phenotypes can be found in (Anno). scale is the standard deviation measure used for normalization. At first standard deviations were computed between replicates for each experiment and afterwards the median of standard deviations was computed.

Usage

data(Interactions)

Format

The format is: List of 4 $ piscore: num [1:282, 1:2, 1:20, 1:2, 1:11, 1:2] -1.814 -2.457 -3.094 -1.448 -0.142 ... ..- attr(*, "dimnames")=List of 6 .. ..$ targetGene : chr [1:282] "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" $ scale : num [1:11] 0.214 0.125 0.139 0.193 0.207 ... $ padj : num [1:282, 1:2, 1:20, 1:2, 1:11] 0.6838 0.4167 0.0949 0.5786 0.7933 ... ..- attr(*, "dimnames")=List of 5 .. ..$ targetGene : chr [1:282] "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" ... $ Anno :List of 3 ..$ target :'data.frame': 282 obs. of 4 variables: .. ..$ ID : chr [1:282] "B1" "B2" "B3" "B4" ... .. ..$ Symbol: chr [1:282] "TDRD6" "PRDM11" "KDM1B" "INTS12" ... .. ..$ Well : chr [1:282] "B1" "B2" "B3" "B4" ... .. ..$ group : chr [1:282] "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(Interactions, package="HD2013SGI")
plot(Interactions$piscore[,1,"SUV39H1",1,"cell.act.m.majoraxis",1])
print(names(which(Interactions$padj[,1,"SUV39H1",1,
                                    "cell.act.m.majoraxis"] <= 0.01)))

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
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Attaching package: 'BiocGenerics'

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

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

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    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
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Attaching package: 'S4Vectors'

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Attaching package: 'limma'

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Attaching package: 'vcd'

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> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/HD2013SGI/Interactions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Interactions
> ### Title: The genetic interaction data.
> ### Aliases: Interactions
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Interactions, package="HD2013SGI")
> plot(Interactions$piscore[,1,"SUV39H1",1,"cell.act.m.majoraxis",1])
> print(names(which(Interactions$padj[,1,"SUV39H1",1,
+                                     "cell.act.m.majoraxis"] <= 0.01)))
 [1] "SETD8"   "TP53"    "BRD4"    "SMARCE1" "PHF5A"   "RUVBL1"  "PRDM15" 
 [8] "HDGF"    "NAP1L5"  "MORF4L1" "CBX1"    "PRDM5"   "BRWD1"   "WDR11"  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>