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UW-GAC / GENESIS

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
https://bioconductor.org/packages/GENESIS
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Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'saddle' not found #114

Closed ruuhsu closed 3 months ago

ruuhsu commented 4 months ago

Hello,

I use the window sliding method to do a SKAT-O test using GENESIS. Here's an error I kept getting and can't seem to find the answer anywhere.

assoc <- assocTestAggregate(iterator, nullmod, test="SKATO")

Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'saddle' not found

I would appreciate if someone could shed some light on this.. thank you!

smgogarten commented 4 months ago

The survey package is required for SKAT-O tests. Please try installing it and restarting your R session.

ruuhsu commented 3 months ago

Hello Stephanie,

Thank you for getting back to me! After activating the survey package, I am still encountering the same issues. I am using R/4.0.5 and I am wondering if other things might be related to this issue. I have reinstalled SKAT package a couple of times as well.

Thank you!

smgogarten commented 3 months ago

R 4.0.5 is several years old at this point, so there may be mismatches between the versions of the packages you are trying to install and your R version. Please try upgrading to the current version of R.