Skip to content

Add alternative solutions to output from ascat.runAscat() #216

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
MartinezRuiz-Carlos wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Add alternative solutions to output from ascat.runAscat() #216

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
da6793e
Add functionality for alternative solutions
MartinezRuiz-Carlos Nov 26, 2025
d7a579a
Remove edit label
MartinezRuiz-Carlos Jan 6, 2026
c236efd
Merge pull request #1 from VanLoo-lab/master
MartinezRuiz-Carlos Jun 9, 2026
ad30994
Fix alt.sol missing bug for manual rho and psi
MartinezRuiz-Carlos Jun 10, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
32 changes: 29 additions & 3 deletions ASCAT/R/ascat.runAscat.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -107,6 +107,14 @@ ascat.runAscat = function(ASCATobj, gamma = 0.55, pdfPlot = FALSE, y_limit = 5,
names(psi) = colnames(n1)
names(goodnessOfFit) = colnames(n1)

# Save alternative solutions
alternative_solutions_list = list()
for (i in 1:length(goodarrays)) {
alternative_solutions_list[[i]] = res[[goodarrays[i]]]$alternative_solutions
}
alternative_solutions <- do.call("rbind", alternative_solutions_list)
alternative_solutions <- as.data.frame(alternative_solutions)

seg = NULL
for (i in 1:length(goodarrays)) {
segje = res[[goodarrays[i]]]$seg
Expand Down Expand Up @@ -177,10 +185,12 @@ ascat.runAscat = function(ASCATobj, gamma = 0.55, pdfPlot = FALSE, y_limit = 5,
seg = NULL
seg_raw = NULL
distance_matrix = NULL
alternative_solutions = NULL
}

return(list(nA = n1, nB = n2, purity = tp, aberrantcellfraction = tp, ploidy = ploidy, psi = psi, goodnessOfFit = goodnessOfFit,
failedarrays = fa, nonaberrantarrays = naarrays, segments = seg, segments_raw = seg_raw, distance_matrix = distance_matrix))
failedarrays = fa, nonaberrantarrays = naarrays, segments = seg, segments_raw = seg_raw, distance_matrix = distance_matrix,
alternative_solutions = alternative_solutions))
}

#' @title runASCAT
Expand Down Expand Up @@ -264,9 +274,23 @@ runASCAT = function(lrr, baf, lrrsegmented, bafsegmented, gender, SNPpos, chromo
nropt = 0
localmin = NULL
optima = list()
alt.sol = data.frame()

if (!failedqualitycheck && is.na(rho_manual)) {

inv.d <- 1/d
alt.ploidy <- cbind(as.numeric(rownames(inv.d)),apply(inv.d,1,max))
alt.cellularity <- cbind(as.numeric(colnames(inv.d)),apply(inv.d,2,max))
alt.p.indx <- which(diff(sign(diff(alt.ploidy[,2]))) == -2) + 1
alt.c.indx <- apply(inv.d[rownames(alt.ploidy[alt.p.indx,,drop=F]),,drop=F],1,function(x){ which(x == max(x))})
if(length(ascat.runAscat) > 0){
alt.sol <- cbind(alt.ploidy[alt.p.indx,1,drop=F], alt.cellularity[alt.c.indx,,drop=F])
colnames(alt.sol) <- c('psi_ploidy', 'rho_aberrant_cell_fraction', 'goodness_of_fit')
alt.sol <- alt.sol[order(alt.sol[,3],decreasing=T),,drop=F]
rownames(alt.sol) <- 1:nrow(alt.sol)
alt.sol[,3] <- (1-((1/alt.sol[,3])/TheoretMaxdist)) * 100
}

# first, try with all filters
for (i in 4:(dim(d)[1]-3)) {
for (j in 4:(dim(d)[2]-3)) {
Expand Down Expand Up @@ -742,7 +766,8 @@ runASCAT = function(lrr, baf, lrrsegmented, bafsegmented, gender, SNPpos, chromo
}

return(list(rho = rho_opt1, psi = psi_opt1, goodnessOfFit = goodnessOfFit_opt1, nonaberrant = nonaberrant,
nA = n1all, nB = n2all, seg = seg, seg_raw = seg_raw, distance_matrix = d))
nA = n1all, nB = n2all, seg = seg, seg_raw = seg_raw, distance_matrix = d,
alternative_solutions = alt.sol))

} else {

Expand All @@ -753,7 +778,8 @@ runASCAT = function(lrr, baf, lrrsegmented, bafsegmented, gender, SNPpos, chromo
dev.off()

warning(paste("ASCAT could not find an optimal ploidy and purity value for sample ", name, ".\n", sep=""))
return(list(rho = NA, psi = NA, goodnessOfFit = NA, nonaberrant = FALSE, nA = NA, nB = NA, seg = NA, seg_raw = NA, distance_matrix = NA))
return(list(rho = NA, psi = NA, goodnessOfFit = NA, nonaberrant = FALSE, nA = NA, nB = NA, seg = NA, seg_raw = NA, distance_matrix = NA,
alternative_solutions = NA))
}

}
Expand Down