Hello,

I'm trying to save the output of pcrelate in gds format using the write.as.gds=TRUE in my command but it doesn't work. I'm getting the following error: Error in .local(gdsobj, ...) : unused argument (write.to.gds = TRUE)

I have installed GENESIS following the Bioconductor instructions: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("GENESIS", version = "3.8")

However when I do the sessionInfo() in R 2.5.0, it shows that the attached package is the GENESIS_2.12.4. I don't know if that makes any difference.

With write.to.gds=FALSE the command works fine but I have a quite large dataset so I would like to save it as gds.

I would appreciate any advice

Best regards Olga

The write.to.gds argument is no longer an option for pcrelate, because the output format has changed. Previously NxN matrices of kinship and IBD sharing coefficients were returned (or written to GDS) as matrices, but this information is now returned as a pairwise table and can be transformed into a matrix (with options for sparsity) with the function pcrelateToMatrix. If you want to in turn save that matrix in a GDS file, you can use the mat2gds function, but that will result in a much larger file than the sparse format provided by the Matrix package.

We have been working with a dataset of ~100,000 samples, and found that the previous version of pcrelate was unable to handle that many samples in any reasonable amount of time (and writing incrementally to GDS files was part of the problem). The best solution for very large sample sizes seems to be to run sample blocks in parallel. Currently that is not documented (as we're still working it out), but the next release of GENESIS will have options for using the functions that are currently internal to pcrelate independently for best performance in large datasets.