Proc Nnpar1way with D option - equivalent in R

I am trying to match SAS output with R. 

I am using Proc Npar1way with D option to get KS test statistic. 
?
Here X is a binary dependent variable and Y is the predicted probabilities;
proc npar1way data = mydata D; class x; var y; run;

When i try this in R 


ks.test(x, fitted(y),alternative = c("two.sided"),exact = NULL) I get very
different result compared to SAS. 

I am new to R. Any help is appreciated. I think i am missing a datastep
maybe ?

Thank you.




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