Error with arguments in getMarkerGenes

[rpolicastro]

If you set 'test.use' in getMarkerGenes to 'wilcox', you get the following error. It will error out in a similar way if you set 'only.pos', 'min.pct', and 'return.thresh' also. Seurat v3 object with ~35000 cells and 2000 features.

seurat <- getMarkerGenes(
        seurat,
        organism="hg",
        column_sample="orig.ident",
        column_cluster="integrated_snn_res.0.4",
        only.pos=FALSE,
        min.pct=0.20,
        thresh.use=log(1.5),
        return.thresh=0.05,
        test.use="wilcox"
)

Get marker genes for samples...
Error in Seurat::FindAllMarkers(temp_seurat, only.pos = only_pos, min.pct = min_pct,  : 
  formal argument "test.use" matched by multiple actual arguments

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.5 (Maipo)

Matrix products: default
BLAS/LAPACK: /gpfs/home/r/p/rpolicas/Carbonate/.conda/envs/cerebro/lib/R/lib/libRblas.so

locale:
[1] C

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

other attached packages:
[1] cerebroPrepare_1.0.0 Seurat_3.0.0        

loaded via a namespace (and not attached):
  [1] nlme_3.1-139         tsne_0.1-3           bitops_1.0-6        
  [4] bit64_0.9-7          progress_1.2.0       RColorBrewer_1.1-2  
  [7] httr_1.4.0           sctransform_0.2.0    tools_3.5.1         
 [10] R6_2.4.0             irlba_2.3.3          KernSmooth_2.23-15  
 [13] BiocGenerics_0.28.0  DBI_1.0.0            lazyeval_0.2.2      
 [16] colorspace_1.4-1     npsurv_0.4-0         prettyunits_1.0.2   
 [19] tidyselect_0.2.5     gridExtra_2.3        curl_3.3            
 [22] bit_1.1-14           compiler_3.5.1       Biobase_2.42.0      
 [25] plotly_4.9.0         caTools_1.17.1.2     scales_1.0.0        
 [28] lmtest_0.9-37        readr_1.3.1          ggridges_0.5.1      
 [31] pbapply_1.4-0        stringr_1.4.0        digest_0.6.18       
 [34] R.utils_2.8.0        pkgconfig_2.0.2      htmltools_0.3.6     
 [37] bibtex_0.4.2         htmlwidgets_1.3      rlang_0.3.4         
 [40] RSQLite_2.1.1        zoo_1.8-5            jsonlite_1.6        
 [43] ica_1.0-2            gtools_3.8.1         dplyr_0.8.0.1       
 [46] R.oo_1.22.0          RCurl_1.95-4.12      magrittr_1.5        
 [49] Matrix_1.2-17        S4Vectors_0.20.1     Rcpp_1.0.1          
 [52] munsell_0.5.0        ape_5.3              reticulate_1.12     
 [55] R.methodsS3_1.7.1    stringi_1.4.3        gbRd_0.4-11         
 [58] MASS_7.3-51.4        gplots_3.0.1.1       Rtsne_0.15          
 [61] plyr_1.8.4           blob_1.1.1           grid_3.5.1          
 [64] parallel_3.5.1       gdata_2.18.0         listenv_0.7.0       
 [67] ggrepel_0.8.1        crayon_1.3.4         lattice_0.20-38     
 [70] cowplot_0.9.4        splines_3.5.1        hms_0.4.2           
 [73] SDMTools_1.1-221.1   pillar_1.3.1         igraph_1.2.4.1      
 [76] stats4_3.5.1         future.apply_1.2.0   reshape2_1.4.3      
 [79] codetools_0.2-16     biomaRt_2.38.0       XML_3.98-1.19       
 [82] glue_1.3.1           lsei_1.2-0           metap_1.1           
 [85] data.table_1.12.2    png_0.1-7            Rdpack_0.11-0       
 [88] gtable_0.3.0         RANN_2.6.1           purrr_0.3.2         
 [91] tidyr_0.8.3          future_1.13.0        assertthat_0.2.1    
 [94] ggplot2_3.1.1        rsvd_1.0.0           survival_2.44-1.1   
 [97] viridisLite_0.3.0    tibble_2.1.1         IRanges_2.16.0      
[100] memoise_1.1.0        AnnotationDbi_1.44.0 cluster_2.0.9       
[103] globals_0.12.4       fitdistrplus_1.0-14  ROCR_1.0-7

[romanhaa]

Yes I think it's because you'll have to use _ instead of .. So, test_use, only_pos, min_pct, and return_thresh. Let me know if that doesn't work either.

[rpolicastro]

That appears to be working. I used the arguments from the documentation for the function, so you may want to update it. Thanks!

[romanhaa]

I updated the manual, thanks for pointing it out.