createNetwork: Create interaction network for top n enriched GO term:coding...

In guldenolgun/NoRCE: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

Create interaction network for top n enriched GO term:coding RNA or GO-term:noncoding RNA interaction. Nodes are GO term and RNA, edges are interactions between them. Each GO-term is annotated and enriched with the mRNAs provided from the input list.

Description

Create interaction network for top n enriched GO term:coding RNA or GO-term:noncoding RNA interaction. Nodes are GO term and RNA, edges are interactions between them. Each GO-term is annotated and enriched with the mRNAs provided from the input list.

Usage

createNetwork(
  mrnaObject,
  type = "pvalue",
  n,
  isNonCode = FALSE,
  takeID = FALSE
)

Arguments

mrnaObject	Output of enrichment results
type	Sort in terms of p-values or FDR. Possible values "pvalue", "padjust"
n	Number of top enrichments
isNonCode	Boolean value that checks whether node of the network is GO-term\& coding or GO-term\& noncoding genes. By default, it is FALSE so node of the network is GO-term\& coding gene. Otherwise, nodes are GO-term\& noncoding genes.
takeID	Boolean value that checks the name decision of the GO/pathway node, GO-term/pathway-term or GO ID-pathway ID. If it is true, name of the GO/pathway node will be GO ID/pathway ID will be used, otherwise, name of the GO/pathway node is GO-term. By default, it is FALSE. It is suggested to used when the GO-term is two long or the GO-term is missing for the custom enrichment database.

Value

Network

guldenolgun/NoRCE documentation built on Oct. 21, 2022, 11:48 a.m.