Prior beliefs for probabilities that a patient fibre is deficient (data from Warren et al. 2020 https://doi.org/10.1038/s41598-020-70885-3)

WarrenPriors.R

# Warren et al. (2020) https://doi.org/10.1038/s41598-020-70885-3

op = par(mfrow=c(2,2))
 # Healthy control subjects (all proteins)
 # C01, C02, C03
 plot(function(x) dbeta(x,1,75),from=0,to=1.0,xlab="pi",ylab="Density",lwd=2, main="Controls")
 abline(v=c(0,1),col="red",lwd=3)
 # Note that we would expect RC defect to manifest in old age, so, in principle, 
 # this prior could change with age of patient at biopsy

 # Patients with nuclear encoded mutation in CI (NDUFB8, NDUFA13/GRIM19)
 # P01 & P02
 plot(function(x) dbeta(x,40,1),from=0,to=1.0,xlab="pi",ylab="Density",lwd=2, main="Nuclear encoded CI")
 abline(v=c(0,1),col="red",lwd=3)
 # Note that we expect all fibres to be affected.  CI proteins go down (clear) however
 # all other proteins go up slightly (less clear).  To compensate?
 # Interestingly many of these fibres have high mito mass
 # So, for all other proteins, same probability of having defect, but effect size much smaller...

 # Patients with single, large-scale mtDNA deletion
 # P03 & P04
 plot(function(x) dbeta(x,6,6),from=0,to=1.0,xlab="pi",ylab="Density",lwd=2, main="Single, large scale deletion")
 abline(v=c(0,1),col="red",lwd=3)
 # We don't usually see mtDNA mutations affecting > 90% of fibres
 # Probably because patients so severely affected have already died?
 # Also, it would be unusual for someone to be classified as a patient and have mutation load < 10%
 # though it could happen and we could potentially identify them by family history

 # Patients with point mutation in tRNA genes
 # P05 - P10
 plot(function(x) dbeta(x,6,6),from=0,to=1.0,xlab="pi",ylab="Density",lwd=2, main="Point mutation in tRNA gene")
 abline(v=c(0,1),col="red",lwd=3)
 # Same reasoning as for deletions (P03 & P04)
par(op)