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n-mounier / bGWAS

R package to perform Bayesian Genome-Wide Association Studies
GNU General Public License v2.0
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! Can't subset `.data` outside of a data mask context #9

Open ChingWen-Chang opened 2 years ago

ChingWen-Chang commented 2 years ago

Dear Ninon,

I encounter an error message when I running bGWAS v1.0.2.. I tried to run your provided data without any modification. However, when I run the below code, there is always an error: ! Can't subset .data outside of a data mask context.

A = bGWAS(name="Test_UsingSmallDataFrame", GWAS = SmallGWAS_Timmers2019, prior_studies = MyStudies, stepwise_threshold = 0.05)

I tried to fix the issue but was unsuccessful. Would you please fix this issue?

Many thanks, 😊 Ching-Wen

Here is the script for the analysis: A = bGWAS(name="Test_UsingSmallDataFrame", GWAS = SmallGWAS_Timmers2019, prior_studies = MyStudies, stepwise_threshold = 0.05)

and here are the log output: <<< Estimation of the prior >>>

Creating the full Z-Matrix

Loading the ZMatrix...

Selecting studies : 4 studies 6,811,310 SNPs

Adding data from the conventional GWAS :

"GWAS" Done! 286,807 SNPs in common between prior studies and the conventional GWAS Computing prior

Calculating the prior chromosome by chromosome...

Chromosome 1 Running regression, Calculating prior estimates for SNPs on this chromosome, Calculating prior standard errors for SNPs on this chromosome, Error: ! Can't subset .data outside of a data mask context. Run rlang::last_error() to see where the error occurred.

PaulTimmers commented 2 years ago

I'm using R version 4.1.3 and managed to fix this problem by replacing .data$. to . in the bind_rows functions inside the compute_prior bGWAS function.