snpgdsSNPListIntersect {SNPRelate} | R Documentation |
Get a common SNP list by comparing their snp id, chromosome, positions and allele frequency if needed.
snpgdsSNPListIntersect(snplist1, snplist2, ..., method=c("position", "exact"), na.rm=TRUE, same.strand=FALSE, verbose=TRUE)
snplist1 |
the SNP list object |
snplist2 |
the SNP list object |
... |
the other SNP list objects |
method |
|
na.rm |
if TRUE, remove mismatched alleles |
same.strand |
if TRUE, assuming the alleles on the same strand |
verbose |
if TRUE, show information |
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 |
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 |
flag... |
|
flag |
flip flag for each common SNP for the n-th GDS file |
Xiuwen Zheng
# 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)