How to save converted file

[manburst]

Dear Sir Now I am learning to use SeqArray package. I am trying to use the package to convert my Exome VCF SNP file into SNPGDS file for SNPrelate package for analysis relatedness. I use seqVCF2GDS(gdsfile, "gds") and seqSNP2GDS(gdsfile, "gds") to convert VCF into GDS then SNP GDS Or convert them back from SNP GDS to VCF file. but how do I save the conveted file? (VCF, GDS and SNP GDS)

Thanks in advance JK.

[zhengxwen]

seqVCF2GDS("your_vcf_file.vcf.gz", "your_output.gds")

The SNPRelate could read the SeqArray GDS file directly, without converting to SNP GDS.

[manburst]

Thank you for quick reply.

And how do I save or export the output file from R environment to local PC?

Thanks JK.