calculatePowerDetectSomatic {PureCN} | R Documentation |
This function calculates the probability of correctly rejecting the null hypothesis that an alt allele is a sequencing error rather than a true (mono-)clonal mutation.
calculatePowerDetectSomatic( coverage, f = NULL, purity = NULL, ploidy = NULL, cell.fraction = 1, error = 0.001, fpr = 5e-07, verbose = TRUE )
coverage |
Mean sequencing coverage. |
f |
Mean expected allelic fraction. If |
purity |
Purity of sample. Only required when |
ploidy |
Ploidy of sample. Only required when |
cell.fraction |
Fraction of cells harboring mutation. Ignored if
|
error |
Estimated sequencing error rate. |
fpr |
Required false positive rate for mutation vs. sequencing error. |
verbose |
Verbose output. |
A list with elements
power |
Power to detect somatic mutations. |
k |
Minimum number of supporting reads. |
f |
Expected allelic fraction. |
Markus Riester
Carter et al. (2012), Absolute quantification of somatic DNA alterations in human cancer. Nature Biotechnology.
purity <- c(0.1,0.15,0.2,0.25,0.4,0.6,1) coverage <- seq(5,35,1) power <- lapply(purity, function(p) sapply(coverage, function(cv) calculatePowerDetectSomatic(coverage=cv, purity=p, ploidy=2, verbose=FALSE)$power)) # Figure S7b in Carter et al. plot(coverage, power[[1]], col=1, xlab="Sequence coverage", ylab="Detection power", ylim=c(0,1), type="l") for (i in 2:length(power)) lines(coverage, power[[i]], col=i) abline(h=0.8, lty=2, col="grey") legend("bottomright", legend=paste("Purity", purity), fill=seq_along(purity)) # Figure S7c in Carter et al. coverage <- seq(5,350,1) power <- lapply(purity, function(p) sapply(coverage, function(cv) calculatePowerDetectSomatic(coverage=cv, purity=p, ploidy=2, cell.fraction=0.2, verbose=FALSE)$power)) plot(coverage, power[[1]], col=1, xlab="Sequence coverage", ylab="Detection power", ylim=c(0,1), type="l") for (i in 2:length(power)) lines(coverage, power[[i]], col=i) abline(h=0.8, lty=2, col="grey") legend("bottomright", legend=paste("Purity", purity), fill=seq_along(purity))