DavisLaboratory / singscore

An R/Bioconductor package that implements a single-sample molecular phenotyping approach
https://davislaboratory.github.io/singscore/
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getStableGenes function not in namespace #28

Closed ruxi closed 3 years ago

ruxi commented 3 years ago

edit: looks like I'm using an older version, Current one is v1.11.1

Hi,

I was going through the singscore tutorial here, everything was fine up until the getStableGenes call. It doesn't look like getStableGenes is in package environment namespace.

> singscore::getStableGenes
Error: 'getStableGenes' is not an exported object from 'namespace:singscore'

the objects that were available in singscore are shown here:

 [1] "generateNull"          "getPvals"              "multiScore"           
 [4] "plotDispersion"        "plotNull"              "plotRankDensity"      
 [7] "plotScoreLandscape"    "projectScoreLandscape" "rankGenes"            
[10] "scoredf_ccle_epi"      "scoredf_ccle_mes"      "scoredf_tcga_epi"     
[13] "scoredf_tcga_mes"      "simpleScore"           "tgfb_expr_10_se"      
[16] "tgfb_gs_dn"            "tgfb_gs_up"            "toy_expr_se"          
[19] "toy_gs_dn"             "toy_gs_up"   

SessionInfo for reference

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Linux Mint 19.3

Matrix products: default
BLAS/LAPACK: /home/ruxi/miniconda3/envs/ruxisnps/lib/libopenblasp-r0.3.6.so

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

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] singscore_1.6.0      GSEABase_1.48.0      graph_1.64.0        
 [4] annotate_1.64.0      XML_3.99-0.3         AnnotationDbi_1.48.0
 [7] IRanges_2.20.2       S4Vectors_0.24.4     Biobase_2.46.0      
[10] BiocGenerics_0.32.0 

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.16.1 locfit_1.5-9.4             
 [3] tidyselect_1.1.0            purrr_0.3.4                
 [5] lattice_0.20-41             colorspace_2.0-0           
 [7] vctrs_0.3.7                 generics_0.1.0             
 [9] utf8_1.2.1                  blob_1.2.1                 
[11] rlang_0.4.10                pillar_1.5.1               
[13] glue_1.4.2                  DBI_1.1.1                  
[15] BiocParallel_1.20.1         bit64_4.0.5                
[17] matrixStats_0.58.0          GenomeInfoDbData_1.2.2     
[19] lifecycle_1.0.0             zlibbioc_1.32.0            
[21] munsell_0.5.0               gtable_0.3.0               
[23] memoise_2.0.0               fastmap_1.1.0              
[25] GenomeInfoDb_1.22.1         fansi_0.4.2                
[27] Rcpp_1.0.6                  xtable_1.8-4               
[29] edgeR_3.28.1                scales_1.1.1               
[31] limma_3.42.2                cachem_1.0.4               
[33] DelayedArray_0.12.3         XVector_0.26.0             
[35] bit_4.0.4                   ggplot2_3.3.3              
[37] dplyr_1.0.5                 GenomicRanges_1.38.0       
[39] grid_3.6.1                  tools_3.6.1                
[41] bitops_1.0-6                magrittr_2.0.1             
[43] RCurl_1.98-1.3              RSQLite_2.2.5              
[45] tibble_3.1.0                crayon_1.4.1               
[47] tidyr_1.1.3                 pkgconfig_2.0.3            
[49] ellipsis_0.3.1              Matrix_1.3-2               
[51] R6_2.5.0                    compiler_3.6.1   
bhuvad commented 3 years ago

Hi @ruxi,

The getStableGenes() function was introduced in a recent version of singscore (v1.8.0) and is not present in the version you are working with. You will need to download R >4.0 and work with the latest version of Bioconductor which in turn will allow you to use the latest version of singscore. Feel free to contact me should you encounter any further issues.

Cheers, Dharmesh