Description Usage Arguments Value Author(s) See Also Examples
View source: R/SNPRelate_Main.r
A list object of SNP information including rs, chr, pos, allele and allele frequency.
1 | snpgdsSNPList(gdsobj, sample.id=NULL)
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gdsobj |
a GDS file object ( |
sample.id |
a vector of sample id specifying selected samples; if NULL, all samples are used |
Return an object of “snpgdsSNPListClass” including the following components:
rs.id |
SNP id |
chromosome |
SNP chromosome index |
position |
SNP physical position in basepair |
allele |
reference / non-ref alleles |
afreq |
allele frequency |
Xiuwen Zheng
snpgdsSNPListIntersect
, snpgdsSNPListStrand
1 2 3 4 5 6 7 8 | # open an example dataset (HapMap)
genofile <- openfn.gds(snpgdsExampleFileName())
# to get a snp list object
snplist <- snpgdsSNPList(genofile)
# close the genotype file
closefn.gds(genofile)
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