rm(list = ls())
library(MEGENA)## Loading required package: doParallel## Loading required package: foreach## Loading required package: iterators## Loading required package: parallel## Loading required package: igraph##
## Attaching package: 'igraph'## The following objects are masked from 'package:stats':
##
## decompose, spectrum## The following object is masked from 'package:base':
##
## unionlibrary(Seurat)## Attaching SeuratObjectlibrary(ggplot2)
library(cowplot)
library(Matrix)Read in Seurat Object file.
obj = readRDS("Output/SeuratObject.RDS")n.cores <- 14;
doPar <- TRUE;
method = "spearman"
FDR.cutoff = 0.05
module.pval = 0.05
hub.pval = 0.05As an example, we will construct MEGENA network for AD cells in cluster 5.
clusterid = 5
obj.cls = obj[,(Idents(obj) == clusterid & obj@meta.data$pathologic.diagnosis.of.AD == 'YES')]
# remove unexpressed genes
min.cells = ncol(obj.cls) * 0.05 # require at least 5% of cells expressed (~ 100 cells)
cnt = GetAssayData(obj.cls,slot = "counts")
nc = rowSums(cnt >= 1E-320,na.rm = TRUE)
ii = which(nc >= min.cells) # index of expressed genes
print(length(ii))## [1] 5853# remove noisy cells
min.genes = 100;
ng = colSums(cnt[ii,] > 1E-320,na.rm = TRUE)
jj = which(ng >= min.genes)
print(length(jj))## [1] 2047datExpr = GetAssayData(obj.cls,slot = "data")[ii,jj]Prepare output directory.
outdir = paste0('MEGENA/Cluster_', clusterid)
if(!file.exists(outdir)) dir.create(outdir, recursive = TRUE)
setwd(outdir)Calculate pairwise correlation.
ijw <- calculate.correlation(datExpr = as.matrix(datExpr), doPerm = 10, method = method, FDR.cutoff = FDR.cutoff)## i = 1
## i = 2
## i = 3
## i = 4
## i = 5
## i = 6
## i = 7
## i = 8
## i = 9
## i = 10
## - outputting correlation results...Prep for parallelization prior to the PFN.
if (doPar)
{
cl = parallel::makeCluster(n.cores)
doParallel::registerDoParallel(cl)
# check how many workers are there
cat(paste("number of cores to use:", foreach::getDoParWorkers(), "\n"))
}## number of cores to use: 14Calculate PFN.
el <- calculate.PFN(ijw[, 1:3], doPar = doPar, num.cores = n.cores)## ####### PFN Calculation commences ########
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## [1] "676 out of 17553 has been included."
## [1] "866 out of 17553 has been included."
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## [1] "Performing parallel quality checks on 14000"
## [1] "Qualified edges: 2745"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "4971 out of 17553 has been included."
## [1] "Performing parallel quality checks on 14000"
## [1] "Qualified edges: 1344"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "6867 out of 17553 has been included."
## [1] "Performing parallel quality checks on 14000"
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## [1] "8465 out of 17553 has been included."
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## [1] "8802 out of 17553 has been included."
## [1] "Performing parallel quality checks on 14000"
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## [1] "9615 out of 17553 has been included."
## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "10299 out of 17553 has been included."
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "10915 out of 17553 has been included."
## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "Performing parallel quality checks on 14000"
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## [1] "15931 out of 17553 has been included."
## [1] "Performing parallel quality checks on 5641"
## [1] "Qualified edges: 0"
## [1] "15931 out of 17553 has been included."write.table(el, file = "MEGENA_Network.txt", sep = "\t", row.names = FALSE, col.names = TRUE, quote = FALSE)
rm(ijw)Do multiscale clustering.
g <- graph.data.frame(el,directed = F)
MEGENA.output <- do.MEGENA(g,
mod.pval = module.pval, hub.pval = hub.pval, remove.unsig = TRUE,
min.size = 20,#max.size = vcount(g)/2,
doPar = TRUE, num.cores = n.cores, n.perm = 100,
save.output = TRUE)## Commence multiscale clustering....
## Calculating distance metric and similarity...
## iteration:1
## - #. tested:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,
## - #. of split:2
## - assess improvements over compactness
## iteration:2
## - #. tested:2
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,
## - #. of split:72
## - assess improvements over compactness
## iteration:3
## - #. tested:74
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,
## - #. of split:54
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,
## - #. of split:11
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,
## - #. of split:1
## - k=2,3,4,5,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,
## - #. of split:11
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,
## - #. of split:11
## - assess improvements over compactness
## - k=2,3,4,
## - #. of split:1
## - k=2,3,4,5,6,7,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,
## - #. of split:6
## - assess improvements over compactness
## - k=2,3,4,5,6,7,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,
## - #. of split:1
## - k=2,3,4,5,6,7,8,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,
## - #. of split:3
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,
## - #. of split:1
## - k=2,3,4,5,6,7,8,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,
## - #. of split:1
## - k=2,3,4,5,6,7,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,
## - #. of split:1
## - k=2,3,4,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,
## - #. of split:1
## - k=2,3,4,5,6,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,
## - #. of split:1
## - k=2,3,4,5,6,7,8,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,
## - #. of split:0
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,
## - #. of split:1
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,4,5,6,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,6,7,
## - #. of split:1
## iteration:4
## - #. tested:123
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,
## - #. of split:3
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,
## - #. of split:4
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,
## - #. of split:1
## - k=2,3,4,
## - #. of split:1
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,
## - #. of split:1
## - k=2,3,4,5,6,
## - #. of split:1
## - k=2,3,4,5,6,7,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,
## - #. of split:1
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,
## - #. of split:1
## - k=2,3,4,5,6,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,
## - #. of split:1
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,6,
## - #. of split:0
## - k=2,3,4,5,6,7,8,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,
## - #. of split:1
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,
## - #. of split:1
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,
## - #. of split:5
## - assess improvements over compactness
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,
## - #. of split:1
## - k=2,3,4,5,6,7,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,6,7,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,
## - #. of split:10
## - assess improvements over compactness
## - k=2,3,4,5,6,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,
## - #. of split:1
## - k=2,3,4,5,6,7,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,
## - #. of split:1
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,
## - #. of split:0
## - k=2,3,4,5,6,7,8,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,
## - #. of split:1
## - k=2,3,4,5,6,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,
## - #. of split:1
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,
## - #. of split:1
## - k=2,3,4,5,6,
## - #. of split:1
## - k=2,3,4,5,6,7,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,4,5,6,7,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,4,
## - #. of split:1
## - k=2,3,4,5,6,7,
## - #. of split:0
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,4,5,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## iteration:5
## - #. tested:55
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,
## - #. of split:1
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,
## - #. of split:1
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,
## - #. of split:1
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,4,5,6,7,
## - #. of split:1
## - k=2,3,4,5,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,
## - #. of split:1
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,
## - #. of split:1
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,
## - #. of split:1
## - k=2,3,4,5,6,
## - #. of split:1
## - k=2,3,4,5,6,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,6,7,8,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,
## - #. of split:1
## - k=2,3,4,5,6,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,
## - #. of split:1
## - k=2,3,4,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,
## - #. of split:1
## - k=2,3,4,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,8,
## - #. of split:0
## - k=2,3,4,5,6,7,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,
## - #. of split:1
## - k=2,3,4,5,6,7,
## - #. of split:0
## - k=2,3,4,5,6,
## - #. of split:0
## - k=2,3,4,
## - #. of split:1
## - k=2,3,4,5,6,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,
## - #. of split:2
## - assess improvements over compactness
## - k=2,3,4,5,6,7,
## - #. of split:1
## - k=2,3,4,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,
## - #. of split:1
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## iteration:6
## - #. tested:9
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,
## - #. of split:1
## - k=2,3,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,
## - #. of split:0
## - k=2,3,4,
## - #. of split:0
## - k=2,3,4,5,
## - #. of split:0
## Commence MHA...
## Calculating hub significance.....
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## Identifying similar scales....
## - Calculating within-module degree profiles.....
## K.max:20
## Cluster scales based on degree profiles...
## k = 2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,## - identified: 2
## Identifying hub genes significant in each scale level...## Assigning module/KDA membership
## Calculating node topological propertiesSave MEGENA analysis object in a file.
save(MEGENA.output, file = "MEGENA_output.RData")sessionInfo()## R version 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
##
## Matrix products: default
## BLAS/LAPACK: /hpc/packages/minerva-centos7/intel/parallel_studio_xe_2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] Matrix_1.3-4 cowplot_1.1.1 ggplot2_3.3.5 SeuratObject_4.0.2
## [5] Seurat_4.0.5 MEGENA_1.3.7 igraph_1.2.8 doParallel_1.0.16
## [9] iterators_1.0.13 foreach_1.5.1
##
## loaded via a namespace (and not attached):
## [1] Rtsne_0.15 colorspace_2.0-2 deldir_1.0-6
## [4] ellipsis_0.3.2 class_7.3-17 modeltools_0.2-23
## [7] ggridges_0.5.3 mclust_5.4.7 spatstat.data_2.1-0
## [10] leiden_0.3.7 listenv_0.8.0 farver_2.1.0
## [13] graphlayouts_0.7.1 ggrepel_0.9.1 flexmix_2.3-17
## [16] fansi_0.5.0 codetools_0.2-16 splines_4.0.3
## [19] robustbase_0.93-7 knitr_1.31 polyclip_1.10-0
## [22] jsonlite_1.7.2 ica_1.0-2 cluster_2.1.0
## [25] kernlab_0.9-29 png_0.1-7 uwot_0.1.10
## [28] spatstat.sparse_2.0-0 sctransform_0.3.2 ggforce_0.3.3
## [31] shiny_1.7.1 compiler_4.0.3 httr_1.4.2
## [34] assertthat_0.2.1 fastmap_1.1.0 lazyeval_0.2.2
## [37] later_1.3.0 tweenr_1.0.2 htmltools_0.5.2
## [40] tools_4.0.3 gtable_0.3.0 glue_1.5.0
## [43] reshape2_1.4.4 RANN_2.6.1 dplyr_1.0.7
## [46] Rcpp_1.0.7 scattermore_0.7 vctrs_0.3.8
## [49] nlme_3.1-149 fpc_2.2-9 ggraph_2.0.5
## [52] lmtest_0.9-38 xfun_0.22 stringr_1.4.0
## [55] globals_0.14.0 mime_0.12 miniUI_0.1.1.1
## [58] lifecycle_1.0.1 irlba_2.3.3 goftest_1.2-3
## [61] future_1.22.1 DEoptimR_1.0-8 MASS_7.3-53
## [64] zoo_1.8-9 scales_1.1.1 tidygraph_1.2.0
## [67] spatstat.core_2.3-0 spatstat.utils_2.2-0 promises_1.2.0.1
## [70] RColorBrewer_1.1-2 yaml_2.2.1 reticulate_1.22
## [73] pbapply_1.5-0 gridExtra_2.3 rpart_4.1-15
## [76] reshape_0.8.8 stringi_1.7.5 rlang_0.4.12
## [79] pkgconfig_2.0.3 prabclus_2.3-2 matrixStats_0.61.0
## [82] evaluate_0.14 lattice_0.20-41 tensor_1.5
## [85] ROCR_1.0-11 purrr_0.3.4 patchwork_1.1.1
## [88] htmlwidgets_1.5.4 tidyselect_1.1.1 parallelly_1.28.1
## [91] RcppAnnoy_0.0.19 plyr_1.8.6 magrittr_2.0.1
## [94] R6_2.5.1 generics_0.1.1 DBI_1.1.1
## [97] withr_2.4.2 mgcv_1.8-33 pillar_1.6.4
## [100] fitdistrplus_1.1-6 abind_1.4-5 survival_3.2-7
## [103] nnet_7.3-14 tibble_3.1.6 future.apply_1.8.1
## [106] crayon_1.4.2 KernSmooth_2.23-17 utf8_1.2.2
## [109] spatstat.geom_2.3-0 plotly_4.10.0 rmarkdown_2.6
## [112] viridis_0.6.2 grid_4.0.3 data.table_1.14.2
## [115] digest_0.6.28 diptest_0.75-7 xtable_1.8-4
## [118] tidyr_1.1.4 httpuv_1.6.3 stats4_4.0.3
## [121] munsell_0.5.0 viridisLite_0.4.0