Hi, 
I have a dataset containing approximately 2 million SNPs. The data is in PLINK format. The data conversion was successful except for a warning message "Nan introduced due to coercion". My problem is that I get an error message when I perform a PCA:

"Principal Component Analysis (PCA) on SNP genotypes: Removing 67 non-autosomal SNPs.Error in snpgdsPCA(genofile) : There is no SNP!"


Here is my script:
#load BED files

bed2L<-“/home/2L_hwe_cleaned.bed”

bim2L<-“/home/2L_hwe_cleaned.bim”

fam2L<-“/home/2L_hwe_cleaned.fam”

 

#convert format

snpgdsBED2GDS(bed2L,
bim2L, fam2L, “chr2L”)
#open filegenofile<-openfn.gds(“chr2L”)
#perform pcapca<-snpgdsPCA(genofile)


I would appreciate some help.
Thanks,Danica 		 	   		  
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