annotateNodes: Annotate node regions

View source: R/annotateNodes.R

annotateNodesR Documentation

Annotate node regions

Description

Assigne gene id and gene symbols to node regions by interacted.

Usage

annotateNodes(
  node_regions,
  txdb,
  orgDb,
  upstream = 2000,
  downstream = 500,
  ...
)

Arguments

node_regions

GRanges object represent regions interacted with nodes.

txdb

An object of TxDb to extract gene information

orgDb

An object of OrgDb to extract gene symbols

upstream, downstream

An integer(1) value indicating the number of bases upstream or downstream from the transcription start site. For additional details see promoters.

...

parameter can be passed to genes

Value

GRanges object with gene_id and symbols metadata.

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene) ## for human hg19
library(org.Hs.eg.db) ## used to convert gene_id to gene_symbol
set.seed(123)
node_regions <- createRandomNodes(TxDb.Hsapiens.UCSC.hg19.knownGene)
annotateNodes(node_regions, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db)

jianhong/interactionHub documentation built on April 22, 2022, 12:34 p.m.