getMM: Title Obtain the Module Membership of genes This function...

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

Description

Title Obtain the Module Membership of genes This function works by getting the Pearson correlation between the eigengene of the module and the gene(s).

Usage

getMM(
  net = NULL,
  expr.data.file = NULL,
  tissue,
  genes,
  which.one = "rnaseq",
  silent = F,
  keep.grey = F,
  identicalNames = T,
  alt.gene.index = NULL,
  dupAware = T
)

Arguments

net	The network can be either and object or a file
expr.data.file	Again an object or a file, genes at columns, samples at rows. It is expected that the genes are in the same order as they are expressed in the network net$moduleColors vector. Use this parameter together with the net one and which.one set to "new" for a network which is not in the DDBB.
tissue	A tissue as it can be find in the network DDBB
genes	The gene names. If set to NULL, the MM of all genes in the network is obtained
which.one	The category the network belongs to. If not in the DDBB just ignore it
silent	Set to true if you want no log
keep.grey	Use grey genes too
alt.gene.index	You can pass genes in a different order, use this index order for that

Value

A data.frame with genes and MM values or a list with genes as keys and the MMs as values

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