Question: could not find function "plotQC" in scater package
1
gravatar for moldach
28 days ago by
moldach20
Canada/Montreal/Douglas Mental Health Institute
moldach20 wrote:

When I install the scater package it's not bringing in the plotQC() function. I get this error:

library(scater)
scater::plotQC()

could not find function "plotQC"

This is my sessionInfo():

R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252   
[3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C                   
[5] LC_TIME=English_Canada.1252    

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

other attached packages:
 [1] scater_1.12.2               ggplot2_3.2.1              
 [3] SingleCellExperiment_1.6.0  SummarizedExperiment_1.14.1
 [5] DelayedArray_0.10.0         BiocParallel_1.18.1        
 [7] matrixStats_0.55.0          Biobase_2.44.0             
 [9] GenomicRanges_1.36.1        GenomeInfoDb_1.20.0        
[11] IRanges_2.18.3              S4Vectors_0.22.1           
[13] BiocGenerics_0.30.0        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2               vipor_0.4.5              compiler_3.6.1          
 [4] pillar_1.4.2             XVector_0.24.0           viridis_0.5.1           
 [7] DelayedMatrixStats_1.6.1 BiocNeighbors_1.2.0      bitops_1.0-6            
[10] tools_3.6.1              zlibbioc_1.30.0          packrat_0.5.0           
[13] viridisLite_0.3.0        tibble_2.1.3             gtable_0.3.0            
[16] lattice_0.20-38          pkgconfig_2.0.3          rlang_0.4.0             
[19] Matrix_1.2-17            rstudioapi_0.10          beeswarm_0.2.3          
[22] gridExtra_2.3            GenomeInfoDbData_1.2.1   withr_2.1.2             
[25] dplyr_0.8.3              grid_3.6.1               tidyselect_0.2.5        
[28] glue_1.3.1               R6_2.4.0                 ggbeeswarm_0.6.0        
[31] irlba_2.3.3              BiocSingular_1.0.0       purrr_0.3.3             
[34] magrittr_1.5             scales_1.0.0             rsvd_1.0.2              
[37] assertthat_0.2.1         colorspace_1.4-1         RCurl_1.95-4.12         
[40] lazyeval_0.2.2           munsell_0.5.0            crayon_1.3.4 
scater • 85 views
ADD COMMENTlink modified 28 days ago by Aaron Lun25k • written 28 days ago by moldach20
Answer: could not find function "plotQC" in scater package
3
gravatar for Aaron Lun
28 days ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:

Some time ago I deprecated and then removed the plotQC function because it was just a trivial wrapper around other functions. I don't recall the exact release when this happened, maybe it was deprecated in BioC 3.8 and removed in 3.9.

Why did I do this? Well, for example, if you're going to write:

plotQC(sce, type="highest-exprs")

you might as well just write

plotHighestExprs(sce)

which takes fewer characters and is more explicit anyway.

ADD COMMENTlink modified 28 days ago • written 28 days ago by Aaron Lun25k
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