snpgdsSNPListIntersect: Get a common SNP list between/among SNP list objects

In SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Description

Get a common SNP list by comparing their snp id, chromosome, positions and allele frequency if needed.

Usage

snpgdsSNPListIntersect(snplist1, snplist2, ..., method=c("position", "exact"),
    na.rm=TRUE, same.strand=FALSE, verbose=TRUE)

Arguments

snplist1	the SNP list object snpgdsSNPListClass
snplist2	the SNP list object snpgdsSNPListClass
...	the other SNP list objects
method	"exact": matching by all snp.id, chromosomes, positions and alleles; "position": matching by chromosomes and positions
na.rm	if TRUE, remove mismatched alleles
same.strand	if TRUE, assuming the alleles on the same strand
verbose	if TRUE, show information

Value

Return a list of snpgdsSNPListClass including the following components:

idx1	the indices of common SNPs in the first GDS file
idx2	the indices of common SNPs in the second GDS file
idx...
idxn	the indices of common SNPs in the n-th GDS file
flag2	an integer vector, flip flag for each common SNP for the second GDS file (assuming a value v): bitwAnd(v, 1): 0 – no flip of allele names, 1 – flip of allele names; bitwAnd(v, 2): 0 – on the same strand, 2 – on the different strands, comparing with the first GDS file; bitwAnd(v, 4): 0 – no strand ambiguity, 4 – ambiguous allele names, determined by allele frequencies; NA – mismatched allele names (there is no NA if na.rm=TRUE)
flag...
flagn	flip flag for each common SNP for the n-th GDS file

Author(s)

Xiuwen Zheng

See Also

snpgdsSNPList

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, exactly matching
v <- snpgdsSNPListIntersect(snplist1, snplist2)
names(v)
# "idx1" "idx2"

# a common snp list, matching by position
v <- snpgdsSNPListIntersect(snplist1, snplist2, method="pos")
names(v)
# "idx1"  "idx2"  "flag2"

table(v$flag2, exclude=NULL)


# close the file
snpgdsClose(genofile)

SNPRelate documentation built on Nov. 8, 2020, 5:31 p.m.