'SNF' is not an exported object from 'namespace:liger' about seurat-wrappers HOT 7 CLOSED

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

from seurat-wrappers.

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

from seurat-wrappers.

got same error.

from seurat-wrappers.

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

from seurat-wrappers.

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)
[email protected] <- 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)

from seurat-wrappers.

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.

from seurat-wrappers.

This was addressed in #41

from seurat-wrappers.