pneuvial c3co issues - Githubissues

pneuvial / c3co

Inferring cancer cell clonality from copy-number data

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ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [rbind]

#78 HenrikBengtsson opened 4 years ago
1
ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [data.frame]

#77 HenrikBengtsson opened 4 years ago
0
Handle when failing to converged, e.g. represent as missing values and BIC=NA

#76 HenrikBengtsson opened 5 years ago
0
fitC3co(): "Error in names(fitList) <- Ks: 'names' attribute [5] must be the same length as the vector [3]"

#75 HenrikBengtsson closed 5 years ago
1
Error in if (BIC > bestBIC) { : missing value where TRUE/FALSE needed

#74 HenrikBengtsson closed 5 years ago
0
New RNG version in R-devel (R 3.6.0) breaks package

#73 HenrikBengtsson closed 5 years ago
3
get.W(..., type=2L): Re-implement ridge regularization to control amount of added jitter (currently eps=1e-08)

#72 HenrikBengtsson closed 5 years ago
0
Better handling of the case where K > J in c3co()

#71 pneuvial opened 5 years ago
0
Use pneuvial/c3co.data (was pneuvial/c3co-data)

#70 HenrikBengtsson closed 5 years ago
0
CLEANUP: Calculate Y=Y1+Y2, Z=Z1+Z2, ... outside of positiveFusedLasso()

#69 HenrikBengtsson opened 5 years ago
0
Task: Let the possibility to include an intercept term in the model to describe normal subclones

#68 jchiquet opened 5 years ago
0
BUG: When converged is FALSE in positieFusedLasso(), we should not compute any statistics

#67 jchiquet opened 5 years ago
0
Avoid requiring a normal in buildSubclones() ?

#66 pneuvial opened 5 years ago
0
Centering data and normal tumor subtype modelling

#65 jchiquet opened 5 years ago
1
Inconsistency in get.W: when M = 2, ncol(Z) = 2 x J (and not J)

#64 jchiquet closed 5 years ago
2
NOTE on how rank deficiency in Z is handled in get.W

#63 pneuvial closed 5 years ago
2
TASK: update on 'buildSubclones'

#62 pneuvial closed 5 years ago
2
TASK: reproduce the experiments described in the c3co manuscript

#61 pneuvial opened 5 years ago
0
TASK: challenge fitC3co() with easy and not so easy problems

#60 pneuvial opened 5 years ago
0
HELP: PVE: 'Percentage Variance Explained' -> 'Percentage of Variation Explained'

#59 HenrikBengtsson closed 5 years ago
1
Argument 'type' in call to 'lsei' in get.W: type= 1 calls LINPACK solver; type = 2 calls QP solver with unexpected ridge regularization

#58 jchiquet closed 5 years ago
4
CONSISTENCY: lambda penalty is not on the expected scale in get.Zt

#57 jchiquet closed 5 years ago
1
TASK: Add tests of positiveFusedLasso() where results have been validated analytically

#56 HenrikBengtsson closed 5 years ago
0
AD HOC: positiveFusedLasso() tries to fix rank deficiency automatically

#55 HenrikBengtsson closed 5 years ago
2
TESTS: We don't test initializeZt(..., forceNormal = TRUE)

#54 HenrikBengtsson closed 5 years ago
0
SPEEDUP: Use Matrix::rowSums(m)

#53 HenrikBengtsson closed 5 years ago
0
BUG: get.W throws an error when input contains a single subclone

#52 pneuvial closed 5 years ago
2
TASK: Rename Z fields Zt fields, e.g. `Z1` -> `Z1t`

#51 HenrikBengtsson opened 5 years ago
0
NOTATION: Use same notation for dimension everywhere

#50 HenrikBengtsson closed 5 years ago
0
ROBUSTNESS: Assert finite estimates on W and Z

#49 HenrikBengtsson opened 5 years ago
2
NOTATION: Rename slot 'S' and 'S0' of 'posFused' to 'Z' and 'Z0'

#48 HenrikBengtsson closed 5 years ago
0
NOTE: FACETS example broken (by the 'facets' package?)

#47 pneuvial opened 5 years ago
0
SPEEDUP: get.W() performance tweaks

#46 HenrikBengtsson closed 5 years ago
1
BUG: 'length(x) = 2 > 1' in coercion to 'logical(1)

#45 HenrikBengtsson closed 5 years ago
2
TASK: Add tests of `get.W()` and `get.Z()` where results have been validated analytically

#44 HenrikBengtsson closed 5 years ago
0
TASK: Rename variable `Z` to `Zt` where it is actually `t(Z)`

#43 HenrikBengtsson closed 5 years ago
3
TASK: Unit tests for `get.W()`, `get.Z()`, and `positiveFusedLasso()`

#42 HenrikBengtsson closed 5 years ago
1
TASK: Help pages for `get.W()` and `get.Z()`

#41 HenrikBengtsson closed 5 years ago
0
TASK: Add assertions/sanity checks on input and output dimensions

#40 HenrikBengtsson closed 5 years ago
0
ROBUSTNESS: upgrade positiveFusedLasso() warning to an error?

#39 HenrikBengtsson opened 6 years ago
1
TESTS: "repeatability" tests

#38 HenrikBengtsson closed 5 years ago
2
PARALLELIZATION: fitC3co() is a good candicate for parallelization

#37 HenrikBengtsson opened 6 years ago
1
TASK: Turn c3co() into generic function

#36 HenrikBengtsson opened 6 years ago
1
TASK: Preserve sample and chromosome names

#35 HenrikBengtsson opened 6 years ago
2
HELP: help("mixSubclone") mentions: A matrix of weights in percentage [0,100]

#34 HenrikBengtsson closed 5 years ago
0
HELP: Some of the help pages need some more love

#33 HenrikBengtsson opened 6 years ago
0
Facets -> FACETS

#32 HenrikBengtsson closed 5 years ago
0
Merge `intercept` into `develop`?

#31 HenrikBengtsson closed 5 years ago
1
S4: What was the reason/rationale for using S4?

#30 HenrikBengtsson opened 6 years ago
6
Error in cutree(hc, k = p) : elements of 'k' must be between 1 and 2

#29 HenrikBengtsson opened 6 years ago
4