Error in RunQuantileAlignSNF function

[mittalan]

I am trying to integrate Seurat objects using liter. When I run the sample code from the tutorial, I get an error in the RunQuantileAlignSNF function.

[DCarbonez]

This issue is specific to R 3.6.
Screenshot shows R 3.5.1 on the left hand side & R 3.6.3 on the right hand side.
The liger::SNF function is not in the namespace.

[jw156605]

We recently updated the liger package with a new algorithm that is significantly more efficient than quantileAlignSNF. The function is called quantile_norm. We are working to update the Seurat wrapper so that it works with the new algorithm and will have a fix soon. In the meantime, you can use the seuratToLiger function or use the "counts" matrices from your Seurat object to make a liger object.

[DCarbonez]

Thank you for your answer. Just out of interest: how come this does not occur in the R 3.5, although the liger version is identical?

[mcap91]

Hi, thank you for providing LIGER, and connections with Seurat via SeuratWrappers!

I ran into this exact problem this week, when newly installing LIGER and SeuratWrappers on my VM. This is the solution I found, which works for the time between updates:

(There also seems to be dependency issues, when installing this way)

devtools::install_github("jefferis/RANN@master-L1")
devtools::install_github("MacoskoLab/liger@v0.4.2", force = T)

packageVersion("liger") #should be '0.4.2"

refs:
stackoverflow.com/questions/40179493
github.com/MacoskoLab/liger/issues

If you are running a VM (I am using Ubuntu on google cloud instance), make sure you have java installed using

sudo apt install default-jre

Good luck!

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

other attached packages:
 [1] forcats_0.5.0        stringr_1.4.0        dplyr_0.8.5          purrr_0.3.4          readr_1.3.1         
 [6] tidyr_1.0.2          tibble_3.0.0         tidyverse_1.3.0      R.utils_2.9.2        R.oo_1.23.0         
[11] R.methodsS3_1.8.0    data.table_1.12.8    ggplot2_3.3.0        SeuratWrappers_0.1.0 Seurat_3.1.5        
[16] liger_0.4.2          patchwork_1.0.0.9000 Matrix_1.2-18        cowplot_1.0.0       

loaded via a namespace (and not attached):
  [1] Rtsne_0.15          colorspace_1.4-1    ellipsis_0.3.0      ggridges_0.5.2      mclust_5.4.6       
  [6] fs_1.4.1            rstudioapi_0.11     leiden_0.3.3        listenv_0.8.0       npsurv_0.4-0       
 [11] remotes_2.1.1       ggrepel_0.8.2       riverplot_0.6       fansi_0.4.1         lubridate_1.7.8    
 [16] xml2_1.3.1          codetools_0.2-16    splines_3.6.3       lsei_1.2-0          knitr_1.28         
 [21] jsonlite_1.6.1      broom_0.5.5         ica_1.0-2           cluster_2.1.0       dbplyr_1.4.2       
 [26] png_0.1-7           uwot_0.1.8          sctransform_0.2.1   BiocManager_1.30.10 compiler_3.6.3     
 [31] httr_1.4.1          backports_1.1.6     assertthat_0.2.1    lazyeval_0.2.2      cli_2.0.2          
 [36] htmltools_0.4.0     tools_3.6.3         rsvd_1.0.3          igraph_1.2.5        gtable_0.3.0       
 [41] glue_1.4.0          RANN_2.6.1          reshape2_1.4.4      rappdirs_0.3.1      Rcpp_1.0.4.6       
 [46] cellranger_1.1.0    vctrs_0.2.4         gdata_2.18.0        ape_5.3             nlme_3.1-147       
 [51] iterators_1.0.12    lmtest_0.9-37       xfun_0.13           globals_0.12.5      rvest_0.3.5        
 [56] lifecycle_0.2.0     irlba_2.3.3         gtools_3.8.2        future_1.17.0       MASS_7.3-51.5      
 [61] zoo_1.8-7           scales_1.1.0        hms_0.5.3           doSNOW_1.0.18       RColorBrewer_1.1-2 
 [66] yaml_2.2.1          reticulate_1.15     pbapply_1.4-2       gridExtra_2.3       stringi_1.4.6      
 [71] foreach_1.5.0       caTools_1.18.0      rlang_0.4.5         pkgconfig_2.0.3     bitops_1.0-6       
 [76] lattice_0.20-41     RANN.L1_2.5.0       ROCR_1.0-7          htmlwidgets_1.5.1   tidyselect_1.0.0   
 [81] RcppAnnoy_0.0.16    plyr_1.8.6          magrittr_1.5        R6_2.4.1            snow_0.4-3         
 [86] gplots_3.0.3        generics_0.0.2      DBI_1.1.0           pillar_1.4.3        haven_2.2.0        
 [91] withr_2.1.2         fitdistrplus_1.0-14 survival_3.1-12     future.apply_1.5.0  tsne_0.1-3         
 [96] modelr_0.1.6        crayon_1.3.4        KernSmooth_2.23-16  plotly_4.9.2.1      readxl_1.3.1       
[101] grid_3.6.3          FNN_1.1.3           reprex_0.3.0        digest_0.6.25       munsell_0.5.0      
[106] viridisLite_0.3.0  

[jw156605]

We have created a pull request to update the Seurat wrapper package and tutorial. As soon as the pull request is merged, this problem will be fixed.

[skpalan]

Before closing this issue, just to again remind that now the Seurat wrapper has been updated and ready to use. Refer to our latest tutorial here.