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aertslab / SCopeLoomR

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...
MIT License
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could not find function "get_cellAnnotation" #10

Closed yingyonghui closed 5 years ago

yingyonghui commented 5 years ago

After install the package, I ran the command line "cellInfo <- get_cellAnnotation(loom)". But it showed that "could not find function 'get_cellAnnotation'". Could anyone help me? Thanks!

dweemx commented 5 years ago

Hi @yingyonghui , Did you load the R package ?

library(SCopeLoomR)

Could you also try to run ?SCopeLoomR::get_cellAnnotation

yingyonghui commented 5 years ago

Hi @yingyonghui , Did you load the R package ?

library(SCopeLoomR)

Could you also try to run ?SCopeLoomR::get_cellAnnotation

Thanks for your reply @mase5 , I followed the instruction in [https://rawcdn.githack.com/aertslab/SCENIC/0a4c96ed8d930edd8868f07428090f9dae264705/inst/doc/SCENIC_Running.html] After loading the package and running the command line "get_cellAnnotation(loom)", it ended up with the errors above. I tried ?SCopeLoomR::get_cellAnnotation, but it showed that "No documentation for ‘get_cellAnnotation’ ...", just as the following:

library(SCopeLoomR)

Attaching package: ‘SCopeLoomR’

The following object is masked from ‘package:base’:

flush

?SCopeLoomR::get_cellAnnotation No documentation for ‘get_cellAnnotation’ in specified packages and libraries: you could try ‘??get_cellAnnotation’

dweemx commented 5 years ago

Could you tell which version of SCopeLoomR you have installed ? You can know this by running packageVersion("SCopeLoomR")

yingyonghui commented 5 years ago

Could you tell which version of SCopeLoomR you have installed ? You can know this by running packageVersion("SCopeLoomR")

It shows that the version of SCopeLoomR is 0.3.1. And the version of R is 3.5.1, in an Ubuntu 18.04 platform. Thanks.

yingyonghui commented 5 years ago

Could you tell which version of SCopeLoomR you have installed ? You can know this by running packageVersion("SCopeLoomR")

It shows that the version of SCopeLoomR is 0.3.1. And the version of R is 3.5.1, in an Ubuntu 18.04 platform. Thanks.

I reinstalled SCopeLoomR of version 0.5.0, and it works correctly now. Thanks for your reminder! I think this issue could be closed now.

yuyingrong commented 2 years ago

Just in case someone wonders: I am using SCopeLoomR v.0.13.0, but got the same issue: could not find function "get_cellAnnotation". Then I found that the function now goes by: get_cell_annotation().

yanpinlu commented 2 years ago

Just in case someone wonders: I am using SCopeLoomR v.0.13.0, but got the same issue: could not find function "get_cellAnnotation". Then I found that the function now goes by: get_cell_annotation(). I am using ScopeLoomR v.0.13.0, the same problem you have, can you use it now? How to solve this problem