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hemberg-lab / scRNA.seq.course

Analysis of single cell RNA-seq data course
https://www.singlecellcourse.org
GNU General Public License v3.0
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Revisions to pseudotime chapter #74

Closed davismcc closed 7 years ago

davismcc commented 7 years ago

Small tweaks for updated monocle package.

Remaining issue that attempting to create the CellDataset object for monocle crashes RStudio. Oddly, running R in the terminal has no problem, and the code below, when run in RStudio, works fine:

library(scater)
data("sc_example_counts")
data("sc_example_cell_info")
pd <- new("AnnotatedDataFrame", data = sc_example_cell_info)
fd <- new("AnnotatedDataFrame", data = data.frame(rownames(sc_example_counts)))
rownames(fd) <- rownames(sc_example_counts)
cds <- monocle::newCellDataSet(sc_example_counts, phenoData = pd, featureData = fd)

Frustratingly, the example in the documentation for monocle's newCellDataSet function cannot be run - surprisingly poor practice from the monocle team there!

So I have no idea at this point why monocle is crashing RStudio for the deng data in our example, but I do worry that most of the course participants will be using RStudio and could face this problem too. Perhaps we should contact the monocle authors with a reproducible example?

wikiselev commented 7 years ago

Great stuff, Davis! I think reporting a problem to Monocle is a good idea, can you do that, please?

Regarding monocle2 - is it still the same name? Shall I use library(monocle) or library(monocle2)?

wikiselev commented 7 years ago

Ok, I think I figured it out - it's still the same name.