Description Usage Arguments Value Author(s) See Also Examples
Create a list of candidate SNPs based on specified criteria
1 2 |
gdsobj |
an object of class |
sample.id |
a vector of sample id specifying selected samples;
if |
snp.id |
a vector of snp id specifying selected SNPs;
if |
autosome.only |
if |
remove.monosnp |
if |
maf |
to use the SNPs with ">= maf" only; if |
missing.rate |
to use the SNPs with "<= missing.rate" only;
if |
verbose |
if |
Return a list of snp ids.
Xiuwen Zheng
snpgdsSampMissRate
, snpgdsSNPRateFreq
,
snpgdsLDpruning
1 2 3 4 5 6 7 8 9 | # open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())
snpset <- snpgdsSelectSNP(genofile, maf=0.05, missing.rate=0.95)
length(snpset)
# 7502
# close the genotype file
snpgdsClose(genofile)
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