Last data update: 2014.03.03

 R: Experimental Data and Analysis of the HCT116 Genetic...
HD2013SGI-packageR Documentation

Experimental Data and Analysis of the HCT116 Genetic Interaction Matrix

Description

Experimental Data and Analysis of the HCT116 Genetic Interaction Matrix. This package contains the data and source code for the paper Laufer, Fischer, Billmann, Huber, Boutros, HD2013SGI, 2013.

Details

Package: HD2013SGI
Type: Package
Version: 0.0.3
License: Artistic-2.0
LazyLoad: true
Imports:
Depends: rhdf5, RColorBrewer, gplots, geneplotter, MASS, grid, hwriter, splots, igraph, abind, limma, vcd, LSD
SystemRequirements: GNU make
biocViews: Infrastructure
Built: R 2.15.1; ; 2013-02-14 12:08:09 UTC; unix

The interaction matrix can be loaded by data(Interactions, package="HD2013SGI"). Type ?Interactions to see a documentation of the interaction data.

The vignette of the package can be seen by typing >library("HD2013SGI") >vignette("HD2013SGI") It contains the complete documentation and R-code for the analysis of the data published in the original publication.

All intermediate results are precomputed and can be loaded. the following datasets are available:

featuresPerWell The screen data in screen order
datamatrixfull The phenotype data of all pairwise genetic perturbation experiments before quality control and feature selection
QueryAnnotation Annotation of all the query genes in the screen
TargetAnnotation Annotation of all target genes in the screen
stabilitySelection Results from the feature selection step
datamatrix The phenotype data of all pairwise genetic perturbation experiments after quality control and feature selection
mainEffects
estimated main effects (single knock down effects) nrOfInteractionsPerTarget number of interactions per target gene
Interactions The genetic interaction data (pi-scores, p-values, and annotation)

A number of helper functions are defined in the package and used in the vignette.

HD2013SGIorderDim hclust on one out of three dimensions of an interaction matrix
HD2013SGIHeatmapHuman plotting a heatmap of a three dimensional array of pi-scores (target genes x query genes x features)
HD2013SGImaineffects estimation main effects
HD2013SGIselectByStability feature selection to select features most stable between replicated experiments

Author(s)

Bernd Fischer

Maintainer: Bernd Fischer <bernd.fischer@embl.de>

References

Laufer, Fischer, Billmann, Huber, Boutros, HD2013SGI, 2013.

Examples

data(Interactions, package="HD2013SGI")

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(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/HD2013SGI-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: HD2013SGI-package
> ### Title: Experimental Data and Analysis of the HCT116 Genetic Interaction
> ###   Matrix
> ### Aliases: HD2013SGI-package HD2013SGI
> ### Keywords: package
> 
> ### ** Examples
> 
> data(Interactions, package="HD2013SGI")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO