Description Usage Arguments Value
Title
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | 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")
)
|
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 |
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
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