Module preservation using adjacency matrix (WGCNA)
1
0
Entering edit mode
maya.kappil ▴ 10
@mayakappil-18569
Last seen 21 months ago

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 • 212 views
ADD COMMENT
1
Entering edit mode
@peter-langfelder-4469
Last seen 8 months ago
United States

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

ADD COMMENT

Login before adding your answer.

Traffic: 501 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6