Sample size (non-missing y and X) = 1763, which is < 2000. The small sample adjustment is applied! #23
Description
Loading required package: Matrix
Loading required package: SPAtest
Loading required package: RSpectra
Warning message:
package ‘Matrix’ was built under R version 4.2.2
Check duplicated SNPs in each SNP set
No duplicate
1763 Samples, 52 Sets, 12493 Total SNPs
[1] "SSD and Info files are created!"
1763 Samples, 52 Sets, 12493 Total SNPs
Open the SSD file
Sample size (non-missing y and X) = 1763, which is < 2000. The small sample adjustment is applied!
[1] "The number of Genes: 52"
[1] "Gene MarkersNum CommonMarkersNum RaretMarkersNum GenePvalue VariantPvalue"
Error in SKAT_CommonRare_Robust(AS_GT, obj, kernel = "linear.weighted", :
unused argument (Adjustment = FALSE)
Execution halted
When I use the SKAT_CommonRare_Robust function, and it appears that my sample size is less than 2000, what should I do if I do not want to perform a small sample size adjustment?