Create a SNP list object

Description

A list object of SNP information including rs, chr, pos, allele and allele frequency.

Usage

snpgdsSNPList(gdsobj, sample.id=NULL)

Arguments

Value

Return an object of snpgdsSNPListClass including the following components:

Author(s)

Xiuwen Zheng

See Also

snpgdsSNPListIntersect, snpgdsSNPListStrand

Examples

# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())

# to get a snp list object
snplist <- snpgdsSNPList(genofile)

# close the file
snpgdsClose(genofile)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(SNPRelate)
Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SNPRelate/snpgdsSNPList.Rd_%03d_medium.png", width=480, height=480)
> ### Name: snpgdsSNPList
> ### Title: Create a SNP list object
> ### Aliases: snpgdsSNPList
> ### Keywords: GDS GWAS
> 
> ### ** Examples
> 
> # open an example dataset (HapMap)
> genofile <- snpgdsOpen(snpgdsExampleFileName())
> 
> # to get a snp list object
> snplist <- snpgdsSNPList(genofile)
> 
> # close the file
> snpgdsClose(genofile)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>