beta.data: Beta Data Of SNP Regressed on Causal Variables and Disease

In GMRP: GWAS-based Mendelian Randomization and Path Analyses

Description

Beta data are a matrix dataset consisting of 5 columns: cad, ldl, hdl, tg, and tc with 368 rows.

Usage

data("beta.data")

Format

A data frame with 368 observations on the following 5 variables.

cad

a numeric vector

ldl

a numeric vector

hdl

a numeric vector

tg

a numeric vector

tc

a numeric vector

Details

Beta data are a matrix consisting of regression coefficients of 368 SNPs on cad, ldl, hdl, tg, tc where cad is coronary artery disease, ldl is low-density lipoprotein cholesterol, hdl, high-density lipoprotein cholesterol, tg,triglycerides and tc, total cholesterol in plasma. These 368 SNPs were obtained by using mktable from GWAS meta-analyzed data.

Value

A set of real regression coefficients of 368 SNPs on disease and causal variables.

Source

http://csg.sph.umich.edu//abecasis/public/lipids2013/

\http://www.cardiogramplusc4d.org/downloads/

References

Willer CJ et al. Discovery and refinement of loci associated with lipid levels. Nat. Genet. 2013. doi:10.1038/ng.2797.

\Schunkert, H. et al. 2011. Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nat Genet 43: 333-338.[online]

\Schunkert H, Konig IR, Kathiresan S, Reilly MP, Assimes TL, Holm H et al. Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nat Genet. 2011 43: 333-338.

Examples

data(beta.data)
## maybe str(beta.data) ; plot(beta.data) ...

Example output

Loading required package: diagram
Loading required package: shape
Loading required package: plotrix
Loading required package: GenomicRanges
Loading required package: stats4
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, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb

Attaching package: ‘GMRP’

The following object is masked from ‘package:BiocGenerics’:

    path

Warning message:
Package 'GMRP' is deprecated and will be removed from Bioconductor
  version 3.7 

GMRP documentation built on Nov. 8, 2020, 5:58 p.m.