snpgdsSelectSNP

an object of class <code><a rd-options="" href="/link/SNPGDSFileClass?package=SNPRelate&version=1.6.4" data-mini-rdoc="SNPRelate::SNPGDSFileClass">SNPGDSFileClass</a></code>,
        a SNP GDS file

gdsobj

a vector of sample id specifying selected samples;
        if <code>NULL</code>, all samples will be used

sample.id

a vector of snp id specifying selected SNPs;
        if <code>NULL</code>, all SNPs will be used

snp.id

if <code>TRUE</code>, use autosomal SNPs only; if it is a
        numeric or character value, keep SNPs according to the specified
        chromosome

autosome.only

if <code>TRUE</code>, remove monomorphic SNPs

remove.monosnp

to use the SNPs with ">= maf" only; if <code>NaN</code>,
        no any MAF threshold

to use the SNPs with "<= missing.rate"="" only;="" if="" <code="">NaN, no any missing threshold</=>

missing.rate

verbose


    Create a list of candidate SNPs based on specified criteria


GWAS

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

snpgdsSelectSNP function

an object of class <code><a rd-options='' href='SNPGDSFileClass'>SNPGDSFileClass</a></code>,
        a SNP GDS file

to use the SNPs with "<= missing.rate" only;
        if <code>NaN</code>, no any missing threshold

snpgdsSelectSNP: SNP selection

Description

Usage

Arguments

Value

See Also

Examples