Z1 <= Z2 ?

[pneuvial]

In https://github.com/pneuvial/incas-cn/blob/master/R/getZ.R#L17-L23 we are taking care of the situation where minor CN > major CN in the latent profiles. Does this happen? Hopefully not. If not, then we should rather throw an error than silently swapping minor and major CNs.

[mpierrejean]

This doesn't happen for the simulations but does on real data experiments (probably due to the trick to estimate DoH and then minor and major CNs).
We may put a "warning" at the beginning of the algorithm to warn user that some estimates of Z1 are greater than Z2.

[pneuvial]

Would you mind commenting on what you did to address this issue, and link to a specific commit?

[mpierrejean]

Modification of get.Z.
Remove

Z1 <- sapply(idx, function(ii){
      jj <- which(Z1[,ii]>Z2[,ii])
      Z1[jj, ii] <- Z2[jj, ii]
       return(Z1[,ii])
    })

minor CN > major CN cannot happen if estimates are correctly done.

[pneuvial]

If it cannot happen, then you should add a sanity check that it doesn't, using e.g. stopifnot().
If it may happen in weird case, then you should at least add a warning.

It would also be nice to have a test about this, but I'm not sure how to do that.

[mpierrejean]

Add a warning when Z1 is larger than Z2.
5e91d7d

[mpierrejean]

In most of cases Z1 is larger than Z2 when the optimal number of archetype is reached.
An example is given below, after p>=4 :

set.seed(147)
len <- 500*10
nbClones <- 3
bkps <- list(c(100,250)*10, c(150,400)*10,c(150,400)*10)
regions <- list(c("(1,2)", "(0,2)", "(1,2)"),
  c("(1,1)", "(0,1)", "(1,1)"), c("(0,2)", "(0,1)", "(1,1)"))
dataAnnotTP <- acnr::loadCnRegionData(dataSet="GSE13372_HCC1143", tumorFraction=1)
dataAnnotN <- acnr::loadCnRegionData(dataSet="GSE13372_HCC1143", tumorFraction=0)
datSubClone <- buildSubclones(len, dataAnnotTP, dataAnnotN, nbClones, bkps, regions)
W = rSparseWeightMatrix(15, 3, 0.7)
datList <- mixSubclones(subClones=datSubClone, W)
l1 <- seq(from=1e-8, to=1e-5, length.out=10)
nb.arch <- 2:6
parameters.grid <- list(lambda1=l1, nb.arch=nb.arch) 
res <- c3co(datList, parameters.grid, verbose=FALSE)