addNetworkToDDBB: Title

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

Description

Title

Usage

addNetworkToDDBB(
  netf,
  folder,
  which.one,
  tissue,
  rewrite = F,
  filter = c("GO", "KEGG", "REAC", "HP"),
  ensembl = TRUE,
  do.go = T,
  do.ct = T,
  exclude.iea = T,
  correction.method = "gSCS",
  organism = "hsapiens",
  out.file = paste0(netf, "_gprofiler.csv")
)

Arguments

netf	The RDS file produced by getDownstreamNetwork()
folder	This method will produce enrichment files. This variable indicates where to store them
which.one	Category under which the network should be installed. If new, the category will be created
tissue	A label to designate the network under the category
rewrite	If TRUE and the network is already added with that name under the category, it is overwritten with the new material
filter	gProfiler parameter to indicate which annotation databases to use when assessing for enrichment at the network modules
ensembl	Whether the gene names are indicated as Ensembl ids or Symbols
do.go	If FALSE the annotation databases enrichment is not perfomed
do.ct	If FALSE the cell enrichment is not performed. Note that cell enrichment works fine for brain. Not so good for other tissues or conditions.
exclude.iea	gProfiler parameter to indicate that if FALSE, inferred annotations from GO are not used
correction.method	gProfiler parameter to indicate the p.value adjustment method
organism	gProfiler parameter to indicate the organism upon which genes are defined
out.file	Optional file to allocate the GO enrichment

Value

This method updates the global variable coexp.nets with a new entry to it can be used with the rest of methods of the package

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