Data to run gene set analysis methods

Description

A list including the following components:

arrayData – a data.frame of dimension 119487 rows and 4 columns including P-values, SNP ids, position and chromosome for a GWAS experiment;

geneSets – a GeneSetCollection containing gene Entrez ids;

ldMat – a matrix of dimension 871 x 871 holding linkage disequilibrium values;

indepSNPs – a list containing 302 independent SNP ids;

Usage

geneSetAnalysis

Examples

    data(geneSetAnalysis)
    head(geneSetAnalysis$arrayData)

Results

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GSEABase
Loading required package: annotate
Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

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

    addNode

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cpvSNP/geneSetAnalysis.Rd_%03d_medium.png", width=480, height=480)
> ### Name: geneSetAnalysis
> ### Title: Data to run gene set analysis methods
> ### Aliases: geneSetAnalysis
> ### Keywords: datasets
> 
> ### ** Examples
> 
>     data(geneSetAnalysis)
>     head(geneSetAnalysis$arrayData)
             P        SNP Position chromosome
6361 0.4385530 rs10779772 12686368          1
6362 0.9673862  rs3010868 12686476          1
6363 0.8034737  rs4568844 12687753          1
6364 0.7689260  rs3010872 12691826          1
6365 0.6024674  rs3000873 12692907          1
6366 0.3566909  rs3000864 12697586          1
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>