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Gregor-Mendel-Institute / MultLocMixMod

An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations
http://www.nature.com/ng/journal/v44/n7/full/ng.2314.html
GNU General Public License v3.0
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Error in stats::lsfit(x, Res_H0, intercept = FALSE) : only 0 cases, but 1 variable #10

Open tommydavies opened 2 years ago

tommydavies commented 2 years ago

Hi there,

I am attempting to run GWAS on 88 samples with ~250,00 SNPs. I have formatted all of the tables such that I am sure that there are no issues with the dimensions of the data going into mlmm_cof().

The function is returning this error:

null model done! pseudo-h= 1 Error in stats::lsfit(x, Res_H0, intercept = FALSE) : only 0 cases, but 1 variable Calls: mlmm_cof -> apply -> FUN -> In addition: Warning message: In stats::lsfit(x, Res_H0, intercept = FALSE) : 88 missing values deleted Execution halted

Any help would be appreciated.

visegura commented 2 years ago

Hi, Thanks for your interest in mlmm. The error seems related to the presence of missing values in your dataset, which are not handled by mlmm. Could you please check for this? Best regards, Vincent