Error in ||: 'length = 9' in coercion to 'logical(1)'

[davidnoe-l]

RStudio Version 2024.04.2+764 (2024.04.2+764)
macOS Sonoma 14.4.1 (23E224)

Hi, I am currently trying to follow your deconvolution protocol in Nature on my Mac and am encountering issues during the downstream analysis of my MeDeCom set with FactoryViz. When I load my dataset into FactorViz, I receive the error "Warning: Error in ||: 'length = 9' in coercion to 'logical(1)'." Despite this, I am able to plot the K-Selection, LMCs, and Proportions without any problems. Although Lambda-Selection with FactorViz is not possible, I selected the Lambda value using the plotParameters function from the MeDeCom package and proceeded with my analysis. Similar issues arise during the GO and LOLA enrichment analysis, which I am still able to perform using the individual MeDeCom functions.

Thank you for your effort, the CompEpigen packages are really neat!

Best regards,
David

> library(FactorViz) 
Loading required package: shiny

Attaching package: ‘shiny’

The following objects are masked from ‘package:R.utils’:

    setProgress, validate

The following object is masked from ‘package:R.oo’:

    printStackTrace

Loading required package: shinyFiles
Loading required package: shinythemes
Loading required package: RColorBrewer
Loading required package: DT

Attaching package: ‘DT’

The following objects are masked from ‘package:shiny’:

    dataTableOutput, renderDataTable

Loading required package: RnBeads.mm10
Loading required package: RnBeads.hg38
Loading required package: igraph

Attaching package: ‘igraph’

The following object is masked from ‘package:R.oo’:

    hierarchy

The following object is masked from ‘package:Biostrings’:

    union

The following object is masked from ‘package:XVector’:

    path

The following object is masked from ‘package:GenomicRanges’:

    union

The following object is masked from ‘package:IRanges’:

    union

The following object is masked from ‘package:S4Vectors’:

    union

The following objects are masked from ‘package:BiocGenerics’:

    normalize, path, union

The following object is masked from ‘package:gtools’:

    permute

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

> setwd("/Users/davidnoe-l/Documents/MeDeCom")
> 
> startFactorViz(file.path(getwd(),"MeDeCom","FactorViz_outputs"))

Listening on http://127.0.0.1:6578
[1] "ALL OK"
[1] "Starting table"
[1] "...............................MeDeComSet..........................."
[1] "...............................MeDeComSet_ende..........................."
Warning: Error in ||: 'length = 9' in coercion to 'logical(1)'
  101: eval
  100: eval
   99: withProgress
   98: renderTable
   97: func
   84: renderFunc
   83: output$AnalysisRunParameterTable
    2: shiny::runApp
    1: startFactorViz
Warning: Error in ||: 'length = 5' in coercion to 'logical(1)'
  98: renderUI
  97: func
  84: renderFunc
  83: output$includeStats
   2: shiny::runApp
   1: startFactorViz
Warning: Error in ||: 'length = 2' in coercion to 'logical(1)'
  98: renderUI
  97: func
  84: renderFunc
  83: output$includeStats
   2: shiny::runApp
   1: startFactorViz
Loading required package: GOstats
Loading required package: Category
Loading required package: Matrix

Attaching package: ‘Matrix’

The following object is masked from ‘package:spam’:

    det

The following object is masked from ‘package:S4Vectors’:

    expand

The following objects are masked from ‘package:pracma’:

    expm, lu, tril, triu

Loading required package: graph

Attaching package: ‘graph’

The following objects are masked from ‘package:igraph’:

    degree, edges, intersection

The following object is masked from ‘package:plyr’:

    join

The following object is masked from ‘package:Biostrings’:

    complement



Attaching package: ‘GOstats’

The following object is masked from ‘package:AnnotationDbi’:

    makeGOGraph

Warning in makeValidParams(.Object) : removing duplicate IDs in geneIds
Warning in makeValidParams(.Object) :
  removing duplicate IDs in universeGeneIds
[1] "LMC 1 processed"
Warning in makeValidParams(.Object) : removing duplicate IDs in geneIds
Warning in makeValidParams(.Object) :
  removing duplicate IDs in universeGeneIds
[1] "LMC 2 processed"
Warning in makeValidParams(.Object) : removing duplicate IDs in geneIds
Warning in makeValidParams(.Object) :
  removing duplicate IDs in universeGeneIds
[1] "LMC 3 processed"
Warning in makeValidParams(.Object) : removing duplicate IDs in geneIds
Warning in makeValidParams(.Object) :
  removing duplicate IDs in universeGeneIds
[1] "LMC 4 processed"
Warning in makeValidParams(.Object) : removing duplicate IDs in geneIds
Warning in makeValidParams(.Object) :
  removing duplicate IDs in universeGeneIds
[1] "LMC 5 processed"
Warning: Error in [[: attempt to select less than one element in get1index
  98: renderUI
  97: func
  84: renderFunc
  83: output$metaAnalysisPanel
   2: shiny::runApp
   1: startFactorViz
Warning: Error in if: the condition has length > 1
  173: eval
  172: eval
  171: withProgress
  170: server_env$doMetaPlot
  169: renderPlot
  167: func
  127: drawPlot
  113: <reactive:plotObj>
   97: drawReactive
   84: renderFunc
   83: output$metaPlot
    2: shiny::runApp
    1: startFactorViz
Warning: Error in if: the condition has length > 1
  105: exprFunc
  104: widgetFunc
  103: ::
htmlwidgets
shinyRenderWidget
  102: func
   89: renderFunc
   88: renderFunc
   84: renderFunc
   83: output$goEnrichementTable
    2: shiny::runApp
    1: startFactorViz