Switch allele strand.

Description

To get a logical vector, indicating whether allele references of snplist2 need to be switched, with respect to snplist1.

Usage

snpgdsSNPListStrand(snplist1, snplist2, same.strand=FALSE)

Arguments

Value

a logical vector, where TRUE indiciates the allele references need to be switched, and NA indiciates that locus is not in the common snp list.

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
L <- snpgdsSNPListStrand(snplist1, snplist2)

table(L, exclude=NULL)

# 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/snpgdsSNPListStrand.Rd_%03d_medium.png", width=480, height=480)
> ### Name: snpgdsSNPListStrand
> ### Title: Switch allele strand.
> ### Aliases: snpgdsSNPListStrand
> ### 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
> L <- snpgdsSNPListStrand(snplist1, snplist2)
> 
> table(L, exclude=NULL)
L
FALSE  <NA> 
 9087     1 
> 
> # close the file
> snpgdsClose(genofile)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>