Hello all,
I am trying to perform SKAT to a dataset in RStudio. In order to do that, I first try to generate an SSD file; however I get the following error:
"Check duplicated SNPs in each SNP set
Error in Check_Duplicate(SSD.Info) :
(GENENAMEHERE) has duplicates! Check following variants : ."
How can I get rid of the duplicates and continue this process?
Thanks!
Hi Inci,
under command line you can do a sort followed by uniq to erase duplicates. like that: cat TOTO.bed | sort | uniq > TOTO-UNIQ.bed
fred
Dear İnci,
in R you could try to use unique(). I am not familiar with your data format so I just assume you have a data frame and your columns contain SNPs. Hope this example can help you out:
dta
Dear Patrick Thorwarth ,
Thank you! I have my files in .bed, .bim, .fam and .SetID formats, so i need a method to remove the duplicated SNP. Does this function also work with these data formats?
Thank you!
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