snpgdsSNPListStrand {SNPRelate} | R Documentation

## 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

`snplist1` | the first SNP list object “snpgdsSNPListClass”
`snplist2` | the second SNP list object “snpgdsSNPListClass”
`same.strand` | `TRUE` assuming alleles are on the same strand (e.g., forward strand); otherwise, `FALSE` not assuming whether on the same strand or not

### 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)

[Package SNPRelate version 1.12.2 Index]