Post by wolfemd on Mar 18, 2015 14:48:56 GMT
Greetings,
I usually work with relationship matrices created in R and other software. I would like to fit models using my own matrices using GCTA. My problem has been that GCTA only accepts binary GRMs. I tried the "OmicKriging" package in R, which has a function to write binary GRM files that should be compatible with GCTA. However, it seems that the conversion doesn't work properly. In particular, GCTA complains that "Error: the size of the [/file/path/CustomMatrix.grm.N.bin] file is incomplete?". This despite the fact that I specified the number of SNP in the R function.
GCTA documentation says that the reml analysis should work even without the "N.bin" file, but it doesn't seem to be true. The analysis does not complete or at least it doesn't produce any output.
Any advice leading to the successful use of custom GRMs in GCTA would be awesome.
Thanks,
Marnin
I usually work with relationship matrices created in R and other software. I would like to fit models using my own matrices using GCTA. My problem has been that GCTA only accepts binary GRMs. I tried the "OmicKriging" package in R, which has a function to write binary GRM files that should be compatible with GCTA. However, it seems that the conversion doesn't work properly. In particular, GCTA complains that "Error: the size of the [/file/path/CustomMatrix.grm.N.bin] file is incomplete?". This despite the fact that I specified the number of SNP in the R function.
GCTA documentation says that the reml analysis should work even without the "N.bin" file, but it doesn't seem to be true. The analysis does not complete or at least it doesn't produce any output.
Any advice leading to the successful use of custom GRMs in GCTA would be awesome.
Thanks,
Marnin
