hapmap_geno

A list object including the following components: <code>sample.id</code> -- a vector of sample ids; <code>snp.id</code> -- a vector of SNP ids; <code>snp.position</code> -- a vector of SNP positions; <code>snp.chromosome</code> -- a vector of chromosome indices; <code>snp.allele</code> -- a character vector of ``reference / non-reference''; <code>genotype</code> -- a ``# of SNPs'' X ``# of samples'' genotype matrix.

datasets

Genome-wide association studies (GWAS) are widely used to
investigate the genetic basis of diseases and traits, but they
pose many computational challenges. We developed an R package
SNPRelate to provide a binary format for single-nucleotide
polymorphism (SNP) data in GWAS utilizing CoreArray Genomic
Data Structure (GDS) data files. The GDS format offers the
efficient operations specifically designed for integers with
two bits, since a SNP could occupy only two bits. SNPRelate is
also designed to accelerate two key computations on SNP data
using parallel computing for multi-core symmetric
multiprocessing computer architectures: Principal Component
Analysis (PCA) and relatedness analysis using
Identity-By-Descent measures. The SNP GDS format is also used by the
GWASTools package with the support of S4 classes and generic functions.
The extended GDS format is implemented in the SeqArray package to
support the storage of single nucleotide variations (SNVs),
insertion/deletion polymorphism (indel) and structural variation calls.

Xiuwen Zheng

SNPRelate

Parallel Computing Toolset for Relatedness and Principal Component
Analysis of SNP Data

hapmap_geno function

A list object including the following components:

 <code>sample.id</code> -- a vector of sample ids;

 <code>snp.id</code> -- a vector of SNP ids;

 <code>snp.position</code> -- a vector of SNP positions;

 <code>snp.chromosome</code> -- a vector of chromosome indices;

 <code>snp.allele</code> -- a character vector of ``reference / non-reference'';

 <code>genotype</code> -- a ``# of SNPs'' X ``# of samples'' genotype matrix.

hapmap_geno: SNP genotypes of HapMap samples

Description

Usage

Arguments

Value