Related Issues (20)
- HELP: PVE: 'Percentage Variance Explained' -> 'Percentage of Variation Explained' HOT 1
- TASK: challenge fitC3co() with easy and not so easy problems
- TASK: reproduce the experiments described in the c3co manuscript
- TASK: update on 'buildSubclones' HOT 2
- NOTE on how rank deficiency in Z is handled in get.W HOT 2
- Inconsistency in get.W: when M = 2, ncol(Z) = 2 x J (and not J) HOT 2
- Centering data and normal tumor subtype modelling HOT 1
- Avoid requiring a normal in buildSubclones() ?
- BUG: When converged is FALSE in positieFusedLasso(), we should not compute any statistics
- Task: Let the possibility to include an intercept term in the model to describe normal subclones
- CLEANUP: Calculate Y=Y1+Y2, Z=Z1+Z2, ... outside of positiveFusedLasso()
- Use pneuvial/c3co.data (was pneuvial/c3co-data)
- Better handling of the case where K > J in c3co()
- get.W(..., type=2L): Re-implement ridge regularization to control amount of added jitter (currently eps=1e-08)
- New RNG version in R-devel (R 3.6.0) breaks package HOT 3
- Error in if (BIC > bestBIC) { : missing value where TRUE/FALSE needed
- fitC3co(): "Error in names(fitList) <- Ks: 'names' attribute [5] must be the same length as the vector [3]" HOT 1
- Handle when failing to converged, e.g. represent as missing values and BIC=NA
- ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [data.frame]
- ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [rbind] HOT 1
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