jeremymcrae / recessivestats Goto Github PK

hgnc ="DNAH14"
chrom = "1"
lof_lof = 5
lof_func = 6
probands = c("DDDP00000X", "DDDP00000Y", "DDDP00000Z")
analyse_inherited_enrichment(hgnc, chrom, lof_lof, lof_func, probands)
extracting ddd frequencies
loading DDD vcfs for DNAH14
converting DDD genotypes
tallying DDD allele counts
1:225347187 is non-LoF ref allele G at last base of exon
1:225445820 is non-LoF ref allele G at last base of exon
1:225576193 is non-LoF ref allele G at last base of exon
Error in lof_func + biallelic_lof :
non-numeric argument to binary operator

Wondering if you are using site filters? As letting in too many bad indels will inflate the frameshift/lof frequencies

Firstly, thank you for sharing the code for others to use :o)

Quick question, would you happen to have all the exac allele frequencies pre-computed in a table also that you can share? This would dramatically speed up things, especially for genes like TTN.

Thanks!