WGCNA is not generationg TOMfiles
0
0
Entering edit mode
18 days ago
Nicolas • 0

Hello im having troubles with WGCNA generating the TOMfiles the code aappears to run correctly but whrn i check eh bwnet object it has a TOMfiles NULL value

This is the code im using


gsg <- goodSamplesGenes(t(mcounts))
summary(gsg)
gsg$allOK
table(gsg$goodGenes)
table(gsg$goodSamples)

Wdds <- DESeqDataSetFromMatrix(countData = mcounts,
                              colData = metadata,
                              design = ~ 1)

Wdds75 <- Wdds[rowSums(counts(Wdds) >= 15) >= 8,]
nrow(Wdds75)

Wdds_norm <- vst(Wdds75)

tcounts <- assay(Wdds_norm) %>% 
           t()
power <- c(c(1:10), seq(from = 12, to = 50, by = 2))

sft <- pickSoftThreshold(tcounts,
                         powerVector = power,
                         networkType = "signed",
                         verbose = 5)

sft_data <- sft$fitIndices

a1 <- ggplot(sft_data, aes(Power, SFT.R.sq, label = Power)) +
      geom_point() +
      geom_text(nudge_y = 0.1) +
      geom_hline(yintercept = 0.8, color = "#C21807") + 
      labs(x = "Power", y = "Scale free topology model fit, signed R^2") +
      theme_classic()

a2 <- ggplot(sft_data, aes(Power, mean.k., label = Power)) +
      geom_point() +
      geom_text(nudge_y = 0.1) +
      labs(x = "Power", y = "Mean Conectivity") +
      theme_classic()

grid.arrange(a1, a2, ncol = 2)

tcounts[] <- sapply(tcounts, as.numeric)
soft_power <- 16
temp_cor <- cor
cor <- WGCNA::cor

bwnet <- blockwiseModules(tcounts,
                 maxBlockSize = 15000,
                 TOMType = "signed",
                 power = soft_power,
                 mergeCutHeight = 0.25,
                 numericLabels = FALSE,
                 randomSeed = 1234,
                 verbose = 3)
cor <- temp_cor
module_eigengenes <- bwnet$MEs
head(module_eigengenes)
table(bwnet$colors)

plotDendroAndColors(bwnet$dendrograms[[1]], cbind(bwnet$unmergedColors, bwnet$colors),
                    c("unmerged", "merged"),
                    dendroLabels = FALSE,
                    addGuide = TRUE,
                    hang= 0.03,
                    guideHang = 0.05)

The output from blockwisemodules is this


Calculating module eigengenes block-wise from all genes
   Flagging genes and samples with too many missing values...
    ..step 1
 ..Working on block 1 .
    TOM calculation: adjacency..
    ..will not use multithreading.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
 ....clustering..
 ....detecting modules..
 ....calculating module eigengenes..
 ....checking kME in modules..
     ..removing 1 genes from module 14 because their KME is too low.
  ..reassigning 2 genes from module 1 to modules with higher KME.
  ..reassigning 1 genes from module 5 to modules with higher KME.
 ..merging modules that are too close..
     mergeCloseModules: Merging modules whose distance is less than 0.25
       Calculating new MEs...

The dimentions of my data are 10 14379

WGCNA • 178 views
ADD COMMENT
0
Entering edit mode
ADD REPLY

Login before adding your answer.

Traffic: 1238 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