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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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latest devel seems to be missing FindVariableFeatures() #1239

Closed mforde84 closed 5 years ago

mforde84 commented 5 years ago 
[root@student39 fordemx]# R

R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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  Natural language support but running in an English locale

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> library(Seurat)
Loading required package: ggplot2
Want to understand how all the pieces fit together? See the R for Data
Science book: http://r4ds.had.co.nz/
Loading required package: cowplot

Attaching package: ‘cowplot’

The following object is masked from ‘package:ggplot2’:

    ggsave

Loading required package: Matrix
> FindVariableFeatures()
Error in FindVariableFeatures() : 
  could not find function "FindVariableFeatures"
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /mnt/beegfs/spackroot/opt/spack/linux-centos7-x86_64/gcc-7.4.0/intel-mkl-2019.1.144-gqx2cyva7h6rwu5zbnxmttlzvr45qwgd/compilers_and_libraries_2019.1.144/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so

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

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

other attached packages:
[1] Seurat_2.3.4  Matrix_1.2-16 cowplot_0.9.4 ggplot2_3.1.0

loaded via a namespace (and not attached):
  [1] tsne_0.1-3          segmented_0.5-3.0   nlme_3.1-137       
  [4] bitops_1.0-6        RColorBrewer_1.1-2  httr_1.4.0         
  [7] prabclus_2.2-7      tools_3.5.2         backports_1.1.3    
 [10] irlba_2.3.3         R6_2.4.0            rpart_4.1-13       
 [13] KernSmooth_2.23-15  Hmisc_4.2-0         lazyeval_0.2.1     
 [16] colorspace_1.4-0    trimcluster_0.1-2.1 nnet_7.3-12        
 [19] npsurv_0.4-0        withr_2.1.2         tidyselect_0.2.5   
 [22] gridExtra_2.3       compiler_3.5.2      htmlTable_1.13.1   
 [25] diptest_0.75-7      caTools_1.17.1.2    scales_1.0.0       
 [28] checkmate_1.9.1     lmtest_0.9-36       DEoptimR_1.0-8     
 [31] mvtnorm_1.0-10      robustbase_0.93-3   ggridges_0.5.1     
 [34] pbapply_1.4-0       dtw_1.20-1          proxy_0.4-23       
 [37] stringr_1.4.0       digest_0.6.18       mixtools_1.1.0     
 [40] foreign_0.8-71      R.utils_2.8.0       base64enc_0.1-3    
 [43] pkgconfig_2.0.2     htmltools_0.3.6     bibtex_0.4.2       
 [46] htmlwidgets_1.3     rlang_0.3.1         rstudioapi_0.9.0   
 [49] jsonlite_1.6        zoo_1.8-4           ica_1.0-2          
 [52] mclust_5.4.3        gtools_3.8.1        acepack_1.4.1      
 [55] dplyr_0.8.0.1       R.oo_1.22.0         magrittr_1.5       
 [58] modeltools_0.2-22   Formula_1.2-3       lars_1.2           
 [61] Rcpp_1.0.0          munsell_0.5.0       reticulate_1.11.1  
 [64] ape_5.2             R.methodsS3_1.7.1   stringi_1.4.3      
 [67] gbRd_0.4-11         MASS_7.3-51.1       flexmix_2.3-15     
 [70] gplots_3.0.1.1      Rtsne_0.15          plyr_1.8.4         
 [73] grid_3.5.2          parallel_3.5.2      gdata_2.18.0       
 [76] crayon_1.3.4        doSNOW_1.0.16       lattice_0.20-38    
 [79] splines_3.5.2       SDMTools_1.1-221    knitr_1.22         
 [82] pillar_1.3.1        igraph_1.2.4        fpc_2.1-11.1       
 [85] reshape2_1.4.3      codetools_0.2-16    stats4_3.5.2       
 [88] glue_1.3.1          lsei_1.2-0          metap_1.1          
 [91] latticeExtra_0.6-28 data.table_1.12.0   png_0.1-7          
 [94] Rdpack_0.10-1       foreach_1.4.4       tidyr_0.8.3        
 [97] gtable_0.2.0        RANN_2.6.1          purrr_0.3.1        
[100] kernlab_0.9-27      assertthat_0.2.0    xfun_0.5           
[103] class_7.3-15        survival_2.43-3     tibble_2.0.1       
[106] snow_0.4-3          iterators_1.0.10    cluster_2.0.7-1    
[109] fitdistrplus_1.0-14 ROCR_1.0-7         
>
mojaveazure commented 5 years ago

Hi Martin,

Your session info shows Seurat v2.3.4 loaded instead of Seurat v3. In Seurat v2, the function is called FindVariableGenes; FindVariableFeatures is the Seurat v3 replacement for FIndVariableGenes.

If you're planning on continuing to use Seurat v2, you'll need to switch back to FindVariableGenes; if you want Seurat v3, please see our installation instructions.