Streamline DE machinery

MarioniLab / scran

Clone of the Bioconductor repository for the scran package.

https://bioconductor.org/packages/devel/bioc/html/scran.html

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Streamline DE machinery #42

Closed LTLA closed 5 years ago

LTLA commented 5 years ago

Bring pairwiseWilcox() and pairwiseBinom() under the auspices of findMarkers()
Deprecate overlapExprs(), which is basically just findMarkers() for pairwiseWilcox() anyway.
Add a way to quickly get the top markers for use in marker detection in SingleR.

LTLA commented 5 years ago

Don't forget to add a lfc= option for pairwiseWilcox(); this could probably be co-opted from tol=.

kevinrue commented 5 years ago

[x] return unsorted output from findMarkers. This should allow you to just do the following for collating results into a single table.

markers.pbmc.up <- findMarkers(sce.pbmc, sce.pbmc$cluster, direction="up", log.p=TRUE)
x <- DataFrame(
  row.names = rownames(sce.pbmc),
  lapply(markers.pbmc.up, "[[", i="log.FDR")
  )