getAndPlotNetworkLong: Title Create a WGCNA network + TOM + some plots If you are...

In juanbot/CoExpNets: Co-expression network management based on WGCNA + k-means

Description

Title Create a WGCNA network + TOM + some plots If you are not interested in the k-means or before getting into that you want to have a look at the basic WGCNA network use this method

Usage

getAndPlotNetworkLong(
  expr.data,
  beta,
  net.type = "signed",
  tissue.name = "MyTissue",
  title = NULL,
  additional.prefix = NULL,
  min.cluster.size = 100,
  save.plots = TRUE,
  return.tom = FALSE,
  excludeGrey = FALSE,
  max.k.cutoff = 150,
  r.sq.cutoff = 0.8,
  cor.type = "pearson",
  silent = T
)

Arguments

expr.data	Aan object or a file, genes at columns, samples at rows. The network net$moduleColors vector will be generated as genes are in the data.frame.
beta	If beta is < 0 then it is obtained automatically. You can set your own.
net.type	Either "signed" or "unsigned" for easier or trickier MM values interpretation
tissue.name	The label you want the code to use for naming the network
title	For possible plots
additional.prefix	Something you want to add to the naming of files generated to avoid potential clashes
min.cluster.size	Minimum number of genes for a group of them to be a cluster
save.plots	You want plots?
return.tom	Set this to TRUE if you want the TOM returned with the rest of stuff (it may be really big)
excludeGrey	Discard grey genes from the result network
max.k.cutoff	Connectivity parameter
r.sq.cutoff	Only beta values above this value for the adjusted linear regression model are considered
cor.type	Values in "pearson", "kendall", "spearman"

Value

If all goes well, a network with the following elements (as a list) * MEs will be a matrix with the eigengenes (columns) and the values for each sample (rows) * moduleLabels A vector of labels corresponding to into which cluster each gene is. labels appear in the same order as genes were disposed in the expression data matrix * moduleColors A vector of colors corresponding to into which cluster each gene is. Useful to refer to each module with a color and to signal them at plots. The vector is named with the genes and they appear in the same order as genes were disposed in the expression data matrix beta Is the beta value used type The type of network as in "signed" or "unsigned" geneTree The dendrogram from which the partition was generated

juanbot/CoExpNets documentation built on May 15, 2021, 12:20 p.m.