Get a common SNP list between two SNP list objects

Description

Get a common SNP list by comparing their rs id, chromosome indices and positions.

Usage

snpgdsSNPListIntersect(snplist1, snplist2)

Arguments

Value

Return an object of snpgdsSNPListClass including the following components:

Author(s)

Xiuwen Zheng

See Also

snpgdsSNPList, snpgdsSNPListStrand

Examples

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

# to get a snp list object
snplist1 <- snpgdsSNPList(genofile)
snplist2 <- snpgdsSNPList(genofile)

# a common snp list
snplist <- snpgdsSNPListIntersect(snplist1, snplist2)

summary(snplist$afreq)

# 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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> library(SNPRelate)
Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SNPRelate/snpgdsSNPListIntersect.Rd_%03d_medium.png", width=480, height=480)
> ### Name: snpgdsSNPListIntersect
> ### Title: Get a common SNP list between two SNP list objects
> ### Aliases: snpgdsSNPListIntersect
> ### Keywords: GDS GWAS
> 
> ### ** Examples
> 
> # open an example dataset (HapMap)
> genofile <- snpgdsOpen(snpgdsExampleFileName())
> 
> # to get a snp list object
> snplist1 <- snpgdsSNPList(genofile)
> snplist2 <- snpgdsSNPList(genofile)
> 
> # a common snp list
> snplist <- snpgdsSNPListIntersect(snplist1, snplist2)
> 
> summary(snplist$afreq)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.0000  0.2043  0.5054  0.5056  0.8088  1.0000 
> 
> # close the file
> snpgdsClose(genofile)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>