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FertigLab / CoGAPS

Bayesian MCMC matrix factorization algorithm
https://www.bioconductor.org/packages/release/bioc/html/CoGAPS.html
BSD 3-Clause "New" or "Revised" License
61 stars 17 forks source link

Cut thresholding for PatternMarkers is not working as intended #37

Closed rossinerbe closed 4 years ago

rossinerbe commented 4 years ago

Using the "cut" threshold for the patternMarkers function returns more genes as PatternMarkers than using the "all" threshold. I would guess that the cut thresholded genes are simply being included as an element of the list returned by the patternMarkers function, and I don't know what "cut" is doing.

Example: `data("GIST")

PMList <- patternMarkers(GIST.result, threshold = "all")

PMListCut <- patternMarkers(GIST.result, threshold = "cut")

lapply(PMList$PatternMarkers, length)

lapply(PMListCut$PatternMarkers, length)`