cad.data: boldGWAS Meta-analyzed Data of Coronary Artery Disease

In GMRP: GWAS-based Mendelian Randomization and Path Analyses

Description

cad.data are a matrix dataset consisting of 12 variables such as SNPID, SNP position on chromosomes, allele and alternative allele, allelic frequencies and 1069 SNPs.

Usage

data("cad.data")

Format

A data frame with 1609 observations on the following 12 variables.

SNP

a character vector

chr_pos_b36

a character vector

reference_allele

a character vector

other_allele

a character vector

ref_allele_frequency

a numeric vector

pvalue

a numeric vector

het_pvalue

a numeric vector

log_odds

a numeric vector

log_odds_se

a numeric vector

N_case

a numeric vector

N_control

a numeric vector

model

a character vector

Details

cad.data, also called CARDIoGRAM GWAS, are a meta-analyzed GWAS data from GWAS studies of European descent imputed to HapMap2 involving 22,233 cases and 64,762 controls. The data were downloaded from the following website.

Value

A data sheet consisting of 1609 rows(SNPs) and 12 columns(character vectors such as SNPID and allele, numeric vector such as allele frequency and beta coefficient. See data format above).

Source

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

References

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(cad.data)
## maybe str(cad.data) ; plot(cad.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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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

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