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diazlab / CONICS

CONICS: COpy-Number analysis In single-Cell RNA-Sequencing
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Error in tutorial #8

Closed romagnolid closed 5 years ago

romagnolid commented 5 years ago

https://github.com/diazlab/CONICS/wiki/Tutorial---CONICSmat;---Dataset:-SmartSeq2-scRNA-seq-of-Oligodendroglioma

> vg <- detectVarGenes(suva_expr, 500)
Error in .local(x, ...) : unused argument (span = 0.2)
soerenmueller commented 5 years ago

Hey romagnolid, could you let me know what version of the scran package you have installed? This seems to be a version issue.

"var.fit = scran::trendVar(mat, span=0.2)"

romagnolid commented 5 years ago

Version 1.10.2

Yes, I have the same feeling but after a quick glance at the scran package I couldn't spot anything related to the trendVar function. I'm probably missing something.

pbrazda commented 5 years ago

Hi,

super-exciting package! I was eager to test it :) , but I think this problem is somewhat similar to the previous ones:

vg=detectVarGenes(suva_expr,500) Error: object ‘int_colData’ is not exported by 'namespace:SingleCellExperiment'

(scran 1.10.2)

Any tips? Thanks!

pbrazda commented 5 years ago

W

Hi,

super-exciting package! I was eager to test it :) , but I think this problem is somewhat similar to the previous ones:

vg=detectVarGenes(suva_expr,500) Error: object ‘int_colData’ is not exported by 'namespace:SingleCellExperiment'

(scran 1.10.2)

Any tips? Thanks!

Now, with R version 3.5.2, scran 1.10.2, to vg=detectVarGenes(suva_expr,500)

I also get Error in .local(x, ...) : unused argument (span = 0.2)

soerenmueller commented 5 years ago

Hi all,

thanks for using CONICS :)

It seems in the most recent version of scran the span argument has been removed. I updated the package accordingly. Please install CONICSmat again using

devtools::install_github("diazlab/CONICS/CONICSmat", dep = FALSE)

and restart your R session. After, the error should be fixed.

Cheers, Soren