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GMELab / RV-EXCALIBER

A methodological framework to conduct a calibrated gene-based rare variant association test by leveraging the genome aggregation database (gnomAD) as an external control dataset
GNU General Public License v3.0
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Error with dataframe #7

Closed OmicsS closed 1 year ago

OmicsS commented 1 year ago

Hi,

I am using RV-Excliber on an HPC cluster for an Exome analysis. I used the scripts as described in the documentation and unfortunately I got the following error when using ./get_RVBurdenMatrix_gnomAD_rvexcaliber.clean.sh (step 2): "Error in [.data.frame(dfAll, , c(1: 13, 15, 14)) : undefined columns selected".

I checked the error and this error appears in the R script "get_Varlist_rvexcaliber.R" (line ~ 670: dfAll <- dfAll[,c(1:13,15,14)])).

Information about my inputdata:

I generated plink files from my vcf, which consists many different variants over several chromosomes. The input file is not split into chromosomes, so I used Step 1a normally like in the example:

cd ${rvexcaliber_shell_scripts} bash get_RVBurdenMatrix_internal_rvexcaliber.clean.sh /genetics/inData /genetics/outData MIGen_BioImage_ExS_QC 0.001,0.005 0.01 0.009,0.025 nfe rcc 10

Next I used Step2 like the example:

cd ${rvexcaliber_shell_scripts} bash get_RVBurdenMatrix_gnomAD_rvexcaliber.clean.sh /genetics/outData MIGen_BioImage_ExS_QC 0.001,0.005 0.009,0.025 nfe rcc

I hope you can help me.

Kind regards

rlali commented 1 year ago

Hi @OmicsS,

Thank you for bringing this up. There was a formatting issue with the rcc gnomAD files. The issue has been fixed. Please download the newest version of RV-EXCALIBER withgit and let me know if you encounter any further issues.