serialization of a table from Stranger's multipopulation eQTL report

Description

serialization of a table from Stranger's multipopulation eQTL report

Usage

data(strMultPop)

Format

A data frame with 39649 observations on the following 12 variables.

rsid

a factor with levels rs...

genesym

a factor with levels 37865 39692 ABC1 ABCD2 ABHD4 ACAS2 ...

illv1pid

a factor with levels GI_10047105-S GI_10092611-A GI_10190705-S GI_10567821-S GI_10835118-S GI_10835186-S ...

snpChr

a numeric vector

snpCoordB35

a numeric vector

probeMidCoorB35

a numeric vector

snp2probe

a numeric vector

minuslog10p

a numeric vector

adjR2

a numeric vector

assocGrad

a numeric vector

permThresh

a numeric vector

popSet

a factor with levels CEU-CHB-JPT CEU-CHB-JPT-YRI CHB-JPT

Details

imported from the PDF(!) distributed by Stranger et al as supplement to PMID 17873874

Source

PMID 17873874 supplement

References

PMID 17873874 supplement

Examples

data(strMultPop)
strMultPop[1:2,]

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(GGtools)
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

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: 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: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand, rowMeans, rowSums

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

    colMeans, colSums, expand.grid, rowMeans, rowSums


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

Attaching package: 'GGtools'

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

    getCall

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GGtools/strMultPop.Rd_%03d_medium.png", width=480, height=480)
> ### Name: strMultPop
> ### Title: serialization of a table from Stranger's multipopulation eQTL
> ###   report
> ### Aliases: strMultPop
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(strMultPop)
> strMultPop[1:2,]
       rsid genesym      illv1pid snpChr snpCoordB35 probeMidCoorB35 snp2probe
1   rs11828    LZIC GI_40255081-S      1     9921273         9924542      3269
2 rs1220398    LZIC GI_40255081-S      1     9928605         9924542      4063
  minuslog10p  adjR2 assocGrad permThresh          popSet
1     26.9436 0.4348    0.2801    12.6861 CEU-CHB-JPT-YRI
2     17.3365 0.3062   -0.2576    12.6861 CEU-CHB-JPT-YRI
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>