Errors in projectR method for sparse matrix data

[dimalvovs]

There is a method to run projectR on sparse data, but it fails with an error.

projectR/R/projectR.R

Line 88 in 39b3b0f

setMethod("projectR",signature(data="dgCMatrix",loadings="matrix"),function(

To reproduce:

load("data/p.RNAseq6l3c3t.RData")
load("data/CR.RNAseq6l3c3t.RData")

data <- as(p.RNAseq6l3c3t, "sparseMatrix")
loadings <- CR.RNAseq6l3c3t@featureLoadings
class(data)
class(loadings)

projectR(data, loadings)

[1] "108 row names matched between data and loadings"
[1] "Updated dimension of data: 108 54"
Error in t.default(dataM[[2]]) : argument is not a matrix

It looks like the first bug is that t.default is called instead of Matrix::t on dataM[[2]]. But even if using the correct t, the result still produces an error:

dataNames <- rownames(data)
loadingsNames <- rownames(loadings)

dataM <- geneMatchR(data1=data, data2=loadings, data1Names=dataNames, data2Names=loadingsNames, merge=FALSE)
projection <- MatrixModels:::lm.fit.sparse(Matrix::t(dataM[[2]]), dataM[[1]])

Error in MatrixModels:::lm.fit.sparse(Matrix::t(dataM[[2]]), dataM[[1]]) : 
  incompatible dimensions of (x,y)

[dimalvovs]

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.1.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] CoGAPS_3.22.0       projectR_1.19.01    testthat_3.2.1     
[4] bigmemory_4.6.4     Biobase_2.62.0      BiocGenerics_0.48.1

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3          rstudioapi_0.15.0          
  [3] jsonlite_1.8.8              umap_0.2.10.0              
  [5] magrittr_2.0.3              fs_1.6.3                   
  [7] zlibbioc_1.48.0             vctrs_0.6.5                
  [9] ROCR_1.0-11                 memoise_2.0.1              
 [11] RCurl_1.98-1.14             askpass_1.2.0              
 [13] forcats_1.0.0               progress_1.2.3             
 [15] htmltools_0.5.7             S4Arrays_1.2.0             
 [17] usethis_2.2.2               curl_5.2.0                 
 [19] Rhdf5lib_1.24.1             rhdf5_2.46.1               
 [21] SparseArray_1.2.3           KernSmooth_2.23-22         
 [23] htmlwidgets_1.6.4           desc_1.4.3                 
 [25] plyr_1.8.9                  cachem_1.0.8               
 [27] uuid_1.2-0                  mime_0.12                  
 [29] lifecycle_1.0.4             iterators_1.0.14           
 [31] pkgconfig_2.0.3             Matrix_1.6-5               
 [33] R6_2.5.1                    fastmap_1.1.1              
 [35] GenomeInfoDbData_1.2.11     MatrixGenerics_1.14.0      
 [37] shiny_1.8.0                 digest_0.6.34              
 [39] colorspace_2.1-0            AnnotationDbi_1.64.1       
 [41] S4Vectors_0.40.2            rprojroot_2.0.4            
 [43] RSpectra_0.16-1             pkgload_1.3.4              
 [45] RSQLite_2.3.5               GenomicRanges_1.54.1       
 [47] filelock_1.0.3              fansi_1.0.6                
 [49] httr_1.4.7                  abind_1.4-5                
 [51] compiler_4.3.2              rngtools_1.5.2             
 [53] remotes_2.4.2.1             bit64_4.0.5                
 [55] withr_3.0.0                 doParallel_1.0.17          
 [57] BiocParallel_1.36.0         DBI_1.2.0                  
 [59] viridis_0.6.5               pkgbuild_1.4.3             
 [61] gplots_3.1.3                biomaRt_2.58.1             
 [63] tsne_0.1-3.1                openssl_2.1.1              
 [65] rappdirs_0.3.3              DelayedArray_0.28.0        
 [67] sessioninfo_1.2.2           caTools_1.18.2             
 [69] gtools_3.9.5                tools_4.3.2                
 [71] httpuv_1.6.14               msigdbr_7.5.1              
 [73] glue_1.7.0                  rhdf5filters_1.14.1        
 [75] promises_1.2.1              grid_4.3.2                 
 [77] gridBase_0.4-7              cluster_2.1.6              
 [79] reshape2_1.4.4              fgsea_1.28.0               
 [81] generics_0.1.3              gtable_0.3.4               
 [83] hms_1.1.3                   data.table_1.15.0          
 [85] xml2_1.3.6                  utf8_1.2.4                 
 [87] XVector_0.42.0              ggrepel_0.9.5              
 [89] foreach_1.5.2               pillar_1.9.0               
 [91] stringr_1.5.1               babelgene_22.9             
 [93] limma_3.58.1                later_1.3.2                
 [95] dplyr_1.1.4                 BiocFileCache_2.10.1       
 [97] lattice_0.22-5              bit_4.0.5                  
 [99] tidyselect_1.2.0            registry_0.5-1             
[101] SingleCellExperiment_1.24.0 Biostrings_2.70.1          
[103] miniUI_0.1.1.1              bigmemory.sri_0.1.8        
[105] gridExtra_2.3               IRanges_2.36.0             
[107] SummarizedExperiment_1.32.0 stats4_4.3.2               
[109] statmod_1.5.0               NMF_0.26                   
[111] devtools_2.4.5              brio_1.1.4                 
[113] matrixStats_1.2.0           stringi_1.8.3              
[115] codetools_0.2-19            tibble_3.2.1               
[117] BiocManager_1.30.22         cli_3.6.2                  
[119] xtable_1.8-4                reticulate_1.35.0          
[121] munsell_0.5.0               Rcpp_1.0.12                
[123] GenomeInfoDb_1.38.5         dbplyr_2.4.0               
[125] png_0.1-8                   XML_3.99-0.16.1            
[127] parallel_4.3.2              MatrixModels_0.5-3         
[129] ellipsis_0.3.2              blob_1.2.4                 
[131] ggplot2_3.4.4               prettyunits_1.2.0          
[133] ggalluvial_0.12.5           profvis_0.3.8              
[135] urlchecker_1.0.1            bitops_1.0-7               
[137] viridisLite_0.4.2           scales_1.3.0               
[139] purrr_1.0.2                 crayon_1.5.2               
[141] rlang_1.1.3                 KEGGREST_1.42.0            
[143] cowplot_1.1.3               fastmatch_1.1-4 

[parkerstevenson]

Receiving the same error when trying to run projectR() on a sparse dgCMatrix.

Error in MatrixModels:::lm.fit.sparse(t(dataM[[2]]), dataM[[1]]) :
incompatible dimensions of (x,y)

[dimalvovs]

just pasting here in order not to forget

• remove obsolete code and unused variables ie commented code and lines 95 111 112
• refactor parameter checks (eg if(is.na()){... )will fail if something would be passed
• implement sparse lm, e.g. SparseM
• update bioconductor