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

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

Get a common SNP list between/among SNP list objects

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...
idx\code{n}	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...
flag\code{n}	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)

zhengxwen/SNPRelate documentation built on April 16, 2024, 8:42 a.m.