Issues With loomR and Seurat with loom

[lololiam]

Hi,

I posted this issue on the Seurat github as well since it concerns both loomR and Seurat so I thought I'd post it here too.

So these are two separate issues but I imagine they might be related somehow.

I am trying to go through both the intro to loomR as well as the guided clustering of the mouse cell atlas (loom edition).

Regarding the loomR intro, when trying to use apply or map, they throw unused argument errors like:

unused arguments (dataset.use = matrix, display.progress = display.progress)

So I assumed maybe the method had been changed since the writing of the vignette, and I got rid of the error by getting rid of the display progress parameter and changing dataset.use to data=matrix. HOWEVER, after changing this I get the error:

Error in private$reset_batch() : attempt to apply non-function

So, I gave up on that since the rest of the tutorial worked and for what I want to do, Seurat with loom functionality is more relevant anyway and I started going through the loom mouse cell atlas vignette.

I had trouble installing it but got it working by uninstalling Seurat, manually installing onlinePCA, and then installing it as described in the tutorial.

When I attempt to use NormalizeData as follows:

> NormalizeData(object = mca, chunk.size = 1000, scale.factor = 10000, display.progress = FALSE)

I get the error:

Error in FUN(trial, ...) : unused arguments (dataset.use = dataset.use, display.progress = display.progress)

Not sure how to resolve this and if it means the package installed incorrectly or if I'm missing a dependency or something.

If at all relevant
methods(class='loom')
returns all the Seurat methods as shown in the vignette.

Any advice would be greatly appreciated,
Thanks,
Liam

[FionaMoon]

Hi,
Does anyone solve this problem?
I also met the problem above.