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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