Question: Module preservation using adjacency matrix (WGCNA)
0
gravatar for maya.kappil
3 months ago by
maya.kappil10
maya.kappil10 wrote:

Hi,

I'm trying out the CoSplicEx pipeline that feeds into WGCNA (https://github.com/iancuo/cosplicingNetworks). To test module preservation, the script loads adjacency matrices, but I get an error regarding the rownames. Below, I recreate the error using some random matrices. Any insight into what I may not be specifying correctly would be greatly appreciated! Thanks.

> library(WGCNA)

R <- matrix(runif(100), ncol=10) 
R <- (R * lower.tri(R)) + t(R * lower.tri(R)) 
diag(R) <- 1 

colnames(R)<-c("MEST","INHBA","IGF2","H19","GNAS","GRHL1","SNPRN","MEG3","PEG10","CDKN1C")
rownames(R)<-c("MEST","INHBA","IGF2","H19","GNAS","GRHL1","SNPRN","MEG3","PEG10","CDKN1C")

S <- matrix(runif(100), ncol=10) 
S <- (S * lower.tri(S)) + t(S * lower.tri(S)) 
diag(S) <- 1 

colnames(S)<-c("MEST","INHBA","IGF2","H19","GNAS","GRHL1","SNPRN","MEG3","PEG10","CDKN1C")
rownames(S)<-c("MEST","INHBA","IGF2","H19","GNAS","GRHL1","SNPRN","MEG3","PEG10","CDKN1C")

multiData =vector("list",2)

multiData[[1]] =list(data= R)
multiData[[2]] =list(data= S)

names(multiData)=c("Ref","SGA")
checkSets(multiData, checkStructure = FALSE, useSets = NULL)

multiColor =vector("list",2)

multiColor[[1]] =c('blue',"blue","red","red","grey","tan","tan","purple","grey","purple")
multiColor[[2]] =c('blue',"blue","red","red","grey","tan","tan","purple","grey","purple")

names(multiColor)=c("Ref","SGA")

modulePreservIndVsConsensus=modulePreservation(
  multiData,
  multiColor,
  dataIsExpr = F,
  networkType = "unsigned", 
  corFnc = "cor",
  corOptions = "use = 'p'",
  referenceNetworks = 1, 
  nPermutations = 200, 
  includekMEallInSummary = FALSE,
  restrictSummaryForGeneralNetworks = FALSE,
  calculateQvalue = FALSE,
  randomSeed = 45, 
  maxGoldModuleSize = 1000, 
  maxModuleSize = 1000, 
  quickCor = 1, 
  ccTupletSize = 2, 
  calculateCor.kIMall = TRUE,
  useInterpolation = FALSE, 
  checkData = F, 
  greyName = "grey", 
  savePermutedStatistics = FALSE, 
  loadPermutedStatistics = FALSE, 
  permutedStatisticsFile = if (useInterpolation) "permutedStats-intrModules.RData" 
  else "permutedStats-actualModules.RData", 
  plotInterpolation = FALSE, 
  interpolationPlotFile = "modulePreservationInterpolationPlots.pdf", 
  discardInvalidOutput = TRUE,
  verbose = 3, indent = 0)
..unassigned 'module' name: grey
  ..all network sample 'module' name: gold
  ..calculating observed preservation values
Error in make.unique(rownames(datRef)) :
  'names' must be a character vector


> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.9 (Final)

Matrix products: default
BLAS/LAPACK: /hpc/packages/minerva-common/intel/parallel_studio_xe_2018/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so

locale:
[1] C

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

other attached packages:
 [1] WGCNA_1.66                  fastcluster_1.1.25
 [3] dynamicTreeCut_1.63-1       DEXSeq_1.28.0
 [5] RColorBrewer_1.1-2          AnnotationDbi_1.44.0
 [7] DESeq2_1.22.1               SummarizedExperiment_1.12.0
 [9] DelayedArray_0.8.0          matrixStats_0.53.1
[11] GenomicRanges_1.34.0        GenomeInfoDb_1.18.1
[13] IRanges_2.16.0              S4Vectors_0.20.1
[15] Biobase_2.42.0              BiocGenerics_0.28.0
[17] BiocParallel_1.16.0         foreach_1.4.4
[19] forcats_0.4.0               stringr_1.4.0
[21] dplyr_0.7.6                 purrr_0.2.5
[23] readr_1.1.1                 tidyr_0.8.1
[25] tibble_2.0.1                ggplot2_3.1.0
[27] tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] colorspace_1.3-2       hwriter_1.3.2          htmlTable_1.12
 [4] XVector_0.22.0         base64enc_0.1-3        rstudioapi_0.7
 [7] bit64_0.9-7            mvtnorm_1.0-8          lubridate_1.7.4
[10] xml2_1.2.0             codetools_0.2-15       splines_3.5.1
[13] doParallel_1.0.14      robustbase_0.93-1.1    impute_1.56.0
[16] geneplotter_1.60.0     knitr_1.20             Formula_1.2-3
[19] jsonlite_1.5           Rsamtools_1.34.0       broom_0.5.0
[22] annotate_1.60.0        cluster_2.0.7-1        GO.db_3.7.0
[25] rrcov_1.4-4            compiler_3.5.1         httr_1.3.1
[28] backports_1.1.2        assertthat_0.2.0       Matrix_1.2-14
[31] lazyeval_0.2.1         cli_1.0.1              acepack_1.4.1
[34] htmltools_0.3.6        prettyunits_1.0.2      tools_3.5.1
[37] bindrcpp_0.2.2         gtable_0.2.0           glue_1.3.0
[40] GenomeInfoDbData_1.2.0 Rcpp_1.0.1             cellranger_1.1.0
[43] Biostrings_2.50.1      preprocessCore_1.44.0  nlme_3.1-137
[46] iterators_1.0.10       rvest_0.3.2            statmod_1.4.30
[49] XML_3.98-1.12          DEoptimR_1.0-8         MASS_7.3-50
[52] zlibbioc_1.28.0        scales_1.0.0           hms_0.4.2
[55] memoise_1.1.0          gridExtra_2.3          biomaRt_2.38.0
[58] rpart_4.1-13           latticeExtra_0.6-28    stringi_1.3.1
[61] RSQLite_2.1.1          genefilter_1.64.0      pcaPP_1.9-73
[64] checkmate_1.8.5        rlang_0.3.1            pkgconfig_2.0.2
[67] bitops_1.0-6           lattice_0.20-35        bindr_0.1.1
[70] htmlwidgets_1.2        robust_0.4-18          bit_1.1-14
[73] tidyselect_0.2.4       plyr_1.8.4             magrittr_1.5
[76] R6_2.4.0               fit.models_0.5-14      Hmisc_4.1-1
[79] DBI_1.0.0              pillar_1.3.1           haven_1.1.2
[82] foreign_0.8-70         withr_2.1.2            survival_2.42-6
[85] RCurl_1.95-4.11        nnet_7.3-12            modelr_0.1.2
[88] crayon_1.3.4           progress_1.2.0         locfit_1.5-9.1
[91] grid_3.5.1             readxl_1.1.0           data.table_1.12.2
[94] blob_1.1.1             digest_0.6.18          xtable_1.8-2
[97] munsell_0.5.0
wgcna • 99 views
ADD COMMENTlink modified 3 months ago by Peter Langfelder2.1k • written 3 months ago by maya.kappil10
Answer: Module preservation using adjacency matrix (WGCNA)
1
gravatar for Peter Langfelder
3 months ago by
United States
Peter Langfelder2.1k wrote:

Thanks for the report, I will look into the issue. Probably a bug in the code.

ADD COMMENTlink written 3 months ago by Peter Langfelder2.1k
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