'SNF' is not an exported object from 'namespace:liger'

[kaizen89]

I'm having this error (title of the issue) when trying to run RunQuantileAlignSNF and I can't find the cause of the issue

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=fr_FR.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] liger_0.5.0.9000     patchwork_1.0.0      Matrix_1.2-18        cowplot_1.0.0        SeuratWrappers_0.1.0
[6] dplyr_0.8.4          Seurat_3.1.4  

Any help?
Thanks

[KyriakisDimitrios]

The same error as @kaizen89

R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

other attached packages:
[1] RColorBrewer_1.1-2   liger_0.5.0.9000     patchwork_1.0.0      Matrix_1.2-17        cowplot_1.0.0        SeuratWrappers_0.1.0
[7] Seurat_3.1.2        

Thanks

[dannyn66]

Same error using the pbmcsca data set from SeuratData.

I just ran the following:
data("pbmcsca")
pbmcsca <- NormalizeData(pbmcsca)
pbmcsca <- FindVariableFeatures(pbmcsca)
pbmcsca <- ScaleData(pbmcsca, split.by = "Method", do.center = FALSE)
pbmcsca <- RunOptimizeALS(pbmcsca, k = 20, lambda = 5, split.by = "Method")
pbmcsca <- RunQuantileAlignSNF(pbmcsca, split.by = "Method")

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Antergos Linux

other attached packages:
[1] liger_0.5.0.9000 patchwork_1.0.0 Matrix_1.2-17 cowplot_1.0.0 SeuratWrappers_0.1.0
[6] pbmcsca.SeuratData_3.0.0 pbmc3k.SeuratData_3.0.0 hcabm40k.SeuratData_3.0.0 SeuratData_0.2.1 Seurat_3.1.4

[lixin4306ren]

got same error.

[ms-balzer]

same error

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] SeuratWrappers_0.1.0 pbmcsca.SeuratData_3.0.0 ifnb.SeuratData_3.0.0 SeuratData_0.2.1 Seurat_3.1.2 liger_0.5.0.9000 patchwork_1.0.0
[8] Matrix_1.2-18 cowplot_1.0.0 devtools_2.2.1 usethis_1.5.1

[KyriakisDimitrios]

I just did not used the Wrapper in the end. Probably Liger updated the function and wrapper didn't udate it.
I used this and it worked. Then you can just transfer the projection to seurat object again

data.liger <- createLiger(sapply(ob.list, function(data) data[['RNA']]@counts[, colnames(data)]), remove.missing = F) 
data.liger <- liger::normalize(data.liger)
data.liger@var.genes <- var.genes
data.liger <- scaleNotCenter(data.liger)
data.liger <- optimizeALS(data.liger, k = k, lamda = lamda) 
data.liger <- quantileAlignSNF(data.liger, resolution = 1.2) 
data.liger <- runUMAP(data.liger, n_neighbors = n_neighbors, min_dist = 0.3) 

seurat_obj = ligerToSeurat(data.liger, use.liger.genes = T)

[mcap91]

Hi, I answered this here

welch-lab/liger#155

They have updated liger. you need to use liger 0.4.2 to have wrapper functionality, until the wrappers are updated.

[mojaveazure]

This was addressed in #41