SAIGE STEP2 does not accept plink files

[alldayscientess]

Hello,

https://github.com/weizhouUMICH/SAIGE/blob/master/extdata/step2_SPAtests.R does not accept plink files while documentation leads me to believe it should https://saigegit.github.io/SAIGE-doc/docs/single_step2.html. Has something changed in the newer version?

Thank you,

Tess

[alldayscientess]

I received the solution from @kscott-1

https://github.com/saigegit/SAIGE/issues/111#issuecomment-1752973089

This is the file: https://github.com/saigegit/SAIGE/blob/main/extdata/step2_SPAtests.R