annotateNodes: Annotate node regions

In jianhong/GenomicInteractionNodes: A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data

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/GenomicInteractionNodes documentation built on Nov. 5, 2024, 4:20 p.m.