SNPlocations {repfdr} | R Documentation

## Three GWAS studies SNPs locations and data

### Description

`SNPlocations` includes the locations of SNPs in chromosomes 1 to 4. Data was simulated to the SNPs with HAPGEN2 for three studies and a sample of it was taken (Chromosomes 1 to 4) for the examples. The data is summarized as z-scores(transformed p-values, with inverse standard normal cumulative distribution). The z-scores matrix can be download from the web (see example).

### Usage

    data(SNPlocations)

### Format

`SNPlocations` data.frame of 249024 SNPs' names, chromosome number and location on the chromosomes. `zmat` Matrix of 249024 SNPs' z-scores (in rows) in each of the 3 studies (columns).

### Source

See: Su, Zhan, Jonathan Marchini, and Peter Donnelly. "HAPGEN2: simulation of multiple disease SNPs." Bioinformatics 27.16 (2011): 2304-2305.

### Examples

    data(SNPlocations)
    head(SNPlocations)

    ## Not run:
    download.file('http://www.math.tau.ac.il/~ruheller/repfdr_RData/zmat.RData',destfile = "zmat.RData")
    load(file = "zmat.RData")

    input.to.repfdr <- ztobins(zmat, 3, df= 15)
    pbz <- input.to.repfdr$pdf.binned.z
    bz  <- input.to.repfdr$binned.z.mat

    ## End(Not run)

[Package repfdr version 1.2.3 Index]