Differential gene test using ~sm.ns(Pseudotime) in Monocle 3?

[varshatm]

I would like to plot genes that change as a function of pseudotime from the trajectory obtained from Monocle 3. It works fine with Monocle 2 with tSNE and DDRTree reduction. But on applying the function to in Monocle 3 (Reduced with UMAP and SimplePPT graph), it gives an error that "~sm.ns(Pseudotime)" is not found. Also, that negbinomal() is not found. [Expression family used was negbinomial.size()]. However, the same errors occur when changing to negbinomial().

[dwucsf]

Hi, I'm running into this same problem. Were you able to figure out what was wrong?

[varshatm]

Hi,

No, I was not able to figure out what the problem was. I believe the function is still not imported in Monocle 3.

On Mon, Mar 4, 2019, 5:13 PM dwucsf notifications@github.com wrote:

Hi, I'm running into this same problem. Were you able to figure out what was wrong?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cole-trapnell-lab/monocle-release/issues/239#issuecomment-469480352, or mute the thread https://github.com/notifications/unsubscribe-auth/ArjbeIocGY1iV4yNIP0KOHMYGMWaDHRLks5vTba5gaJpZM4ZHGaz .

[ChengxiangQiu]

You can use library(VGAM) to load sm.ns() function

[dwucsf]

Thanks ChengxiangQui. The "sm.ns" error has now been resolved, but the negbinomial.size error persists. Here is the error:

Error in x@family@vfamily %in% c("negbinomial", "negbinomial.size") : trying to get slot "family" from an object of a basic class ("logical") with no slots

Do you know what's wrong?

[ChengxiangQiu]

Sorry that I have no idea, I haven't met the same issue. negbinomial.size() function is also included in the VGAM package.

[dwucsf]

No problem. Thanks!