snpgdsFs fuction/Issue in returning SNP ids list used in the analysis

zhengxwen / SNPRelate

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)

http://www.bioconductor.org/packages/SNPRelate

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snpgdsFs fuction/Issue in returning SNP ids list used in the analysis #43

Closed elenadehnavi closed 6 years ago

elenadehnavi commented 6 years ago

Hi Xiuwen, I'm using SNPRelate package. Using snpgdsFs fuction I can not find the SNP ids used in the analysis which I expect to be returned in out put (manual page 29). Running the example dataset of manual this issue existed. Thanks Elena

zhengxwen commented 6 years ago

     snpgdsFst(gdsobj, population, method=c("W&C84", "W&H02"), sample.id=NULL,
         snp.id=NULL, autosome.only=TRUE, remove.monosnp=TRUE, maf=NaN,
         missing.rate=NaN, with.id=FALSE, verbose=TRUE)

with.id: if ‘TRUE’, the returned value with ‘sample.id’ and ‘sample.id’

You should set with.id=TRUE in snpgdsFst().

elenadehnavi commented 6 years ago

Great! Thanks.