Uses the procona network object,
the data with peptides as columns, samples in rows.
And the power that the net was built at
the number of permutations to do...
Modules are permuted and mean topological overlap
is recorded, constructing the null. The number
of random permutations with mean TO greater than
observed provides the p-value.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(ProCoNA)
Loading required package: WGCNA
Loading required package: dynamicTreeCut
Loading required package: fastcluster
Attaching package: 'fastcluster'
The following object is masked from 'package:stats':
hclust
==========================================================================
*
* Package WGCNA 1.51 loaded.
*
* Important note: It appears that your system supports multi-threading,
* but it is not enabled within WGCNA in R.
* To allow multi-threading within WGCNA with all available cores, use
*
* allowWGCNAThreads()
*
* within R. Use disableWGCNAThreads() to disable threading if necessary.
* Alternatively, set the following environment variable on your system:
*
* ALLOW_WGCNA_THREADS=<number_of_processors>
*
* for example
*
* ALLOW_WGCNA_THREADS=4
*
* To set the environment variable in linux bash shell, type
*
* export ALLOW_WGCNA_THREADS=4
*
* before running R. Other operating systems or shells will
* have a similar command to achieve the same aim.
*
==========================================================================
Attaching package: 'WGCNA'
The following object is masked from 'package:stats':
cor
Loading required package: MSnbase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics
This is MSnbase version 1.20.7
Read '?MSnbase' and references therein for information
about the package and how to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
Loading required package: flashClust
Attaching package: 'flashClust'
The following object is masked from 'package:fastcluster':
hclust
The following object is masked from 'package:stats':
hclust
Attaching package: 'ProCoNA'
The following object is masked from 'package:ProtGenerics':
peptides
The following object is masked from 'package:Biobase':
samples
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ProCoNA/toPermTest.Rd_%03d_medium.png", width=480, height=480)
> ### Name: toPermTest
> ### Title: toPermTest
> ### Aliases: toPermTest toPermTest,proconaNet,numeric-method
>
> ### ** Examples
>
> data(ProCoNA_Data)
> #net1 <- buildProconaNetwork("peptide network", peptideData, pow=12)
> toPermTest(net1, 100)
Permuting module: 1
dim of TOM: 140140
Permuting module: 2
dim of TOM: 130130
Permuting module: 4
dim of TOM: 9595
Permuting module: 3
dim of TOM: 109109
Network Name: peptide network
Number of samples : 60
Number of peptides: 474
Number of modules : 4
Power used : 12
Network Type : signed
ProCoNA version : 0.99.1
>
>
>
>
>
> dev.off()
null device
1
>