ppjeep

Pvalue shows "-nan" in output of gene level association test

3

Most of gene-level outputs are reasonable, but there are a few lines show "-nan" in Pvalue. ### Gene RANGE N_IN--geneFile ${geneF} --kernel skato FORMATIVE NumVar NumPolyVar Q rho Pvalue ILF2...

For gene level models, do they work with rare variants only (i.e., is it required to set --freqUpper 0.05)?

2

1. In the example folder of rvtest package, you did not specify --freqUpper 0.05 in cmd.sh. Here is the example code. If I use --freqUpper 0.05 in the same command,...

1. Could you please add bgen2vcf, bgenFileInfo utitlies into pre-built executable binary package (for Linux 64bit)? 2. In the example folder of rvtest package, you did not specify --freqUpper 0.05...

I am working on the exome aray data (30% common variants and 70% rare variants). When I run EMMAX for the exome array data, it failed. Here is the error...