SNPlocations: Three GWAS studies SNPs locations and data

In shay-y/repfdr: Replicability Analysis for Multiple Studies of High Dimension

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)

shay-y/repfdr documentation built on May 29, 2019, 9:20 p.m.