Hello everyone,

I have a problem running the MIMFA function in the missRows package. The initial creation of the MIDTList object works (mad_filtered_reads is a data.frame and the others are data matrices, just like in the example code of the NCI60 data). The colData storage is a DFrame containing the strata of the subjects.

Now, when I try to run the MIMFA function on the before created midt object, it says undefined columns selected. I would really appreciate any help to get me to run this imputation.

midt <- MIDTList("Transcriptomics" = mad_filtered_reads,"Amino Acids"= amac, "Organic Acids" = orgac, "Microbiome" = mic, colData = storage)
## Output:
##An object of class MIDTList.

##Tables:
##                features individuals miss.indv
##Transcriptomics    10000          24         4
##Amino Acids           22          24         4
##Organic Acids          3          16        12
##Microbiome          4398          20         8

##Strata:
##     bad     good moderate 
##      12        8        8 

midt_mimfa <- MIMFA(midt, ncomp=10, M=30, estimeNC = TRUE) 
## Error:
##Error in `[.data.frame`(mat, , colSeq) : undefined columns selected


sessionInfo( )
##R version 4.0.5 (2021-03-31)
##Platform: x86_64-apple-darwin17.0 (64-bit)
##Running under: macOS Big Sur 10.16

##Matrix products: default
##LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

##locale:
##[1] de_AT.UTF-8/de_AT.UTF-8/de_AT.UTF-8/C/de_AT.UTF-8/de_AT.UTF-8

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

##other attached packages:
## [1] missRows_1.10.0             MultiAssayExperiment_1.16.0 SummarizedExperiment_1.20.0
## [4] GenomicRanges_1.42.0        GenomeInfoDb_1.26.7         IRanges_2.24.1             
## [7] S4Vectors_0.28.1            MatrixGenerics_1.2.1        matrixStats_0.58.0         
##[10] mixOmics_6.14.1             lattice_0.20-44             MASS_7.3-54                
##[13] ggplot2_3.3.3               CancerSubtypes_1.17.1       NMF_0.23.0                 
##[16] Biobase_2.50.0              BiocGenerics_0.36.1         cluster_2.1.2              
##[19] rngtools_1.5                pkgmaker_0.32.2             registry_0.5-1             
##[22] sigclust_1.1.0              readxl_1.3.1                data.table_1.14.0          
##[25] edgeR_3.32.1                limma_3.46.0               

##loaded via a namespace (and not attached):
## [1] bitops_1.0-7                doParallel_1.0.16           RColorBrewer_1.1-2         
## [4] tools_4.0.5                 utf8_1.2.1                  R6_2.5.0                   
## [7] DBI_1.1.1                   colorspace_2.0-1            withr_2.4.2                
##[10] tidyselect_1.1.1            gridExtra_2.3               compiler_4.0.5             
##[13] cli_2.5.0                   DelayedArray_0.16.3         scales_1.1.1               
##[16] stringr_1.4.0               digest_0.6.27               XVector_0.30.0             
##[19] pkgconfig_2.0.3             rlang_0.4.11                rstudioapi_0.13            
##[22] impute_1.64.0               generics_0.1.0              gtools_3.9.2               
##[25] BiocParallel_1.24.1         dplyr_1.0.6                 RCurl_1.98-1.3             
##[28] magrittr_2.0.1              GenomeInfoDbData_1.2.4      Matrix_1.3-3               
##[31] Rcpp_1.0.6                  munsell_0.5.0               fansi_0.4.2                
##[34] lifecycle_1.0.0             stringi_1.6.2               zlibbioc_1.36.0            
##[37] plyr_1.8.6                  grid_4.0.5                  ggrepel_0.9.1              
##[40] crayon_1.4.1                splines_4.0.5               locfit_1.5-9.4             
##[43] pillar_1.6.1                igraph_1.2.6                corpcor_1.6.9              
##[46] reshape2_1.4.4              codetools_0.2-18            glue_1.4.2                 
##[49] iCluster_2.1.0              BiocManager_1.30.15         vctrs_0.3.8                
##[52] foreach_1.5.1               cellranger_1.1.0            gtable_0.3.0               
##[55] purrr_0.3.4                 tidyr_1.1.3                 assertthat_0.2.1           
##[58] gridBase_0.4-7              xtable_1.8-4                ConsensusClusterPlus_1.54.0
##[61] RSpectra_0.16-0             survival_3.2-11             rARPACK_0.11-0             
##[64] tibble_3.1.1                iterators_1.0.13            ellipse_0.4.2              
##[67] ellipsis_0.3.2