MOCHA (version 1.1.0)

annotateTiles: annotateTiles

Description

annotateTiles annotates a set of sample-tile matrices given with gene annotations. Details on TxDb and Org annotation packages and available annotations can be found at Bioconductor: https://bioconductor.org/packages/3.15/data/annotation/

Usage

annotateTiles(Obj, TxDb = NULL, Org = NULL, promoterRegion = c(2000, 100))

Value

Obj, the input data structure with added gene annotations (whether GRanges or SampleTileObj)

Arguments

Obj

A RangedSummarizedExperiment generated from getSampleTileMatrix, containing TxDb and Org in the metadata. This may also be a GRanges object.

TxDb

The annotation package for TxDb object for your genome. Optional, only required if Obj is a GRanges.

Org

The genome-wide annotation for your organism. Optional, only required if Obj is a GRanges.

promoterRegion

Optional list containing the window size in basepairs defining the promoter region. The format is (upstream, downstream). Default is (2000, 100).

Examples

if (FALSE) {
library(TxDb.Hsapiens.UCSC.hg38.refGene)
library(org.Hs.eg.db)
SampleTileMatricesAnnotated <- MOCHA::annotateTiles(
  SampleTileMatrices,
  TxDb = TxDb.Hsapiens.UCSC.hg38.refGene,
  Org = org.Hs.eg.db
)
}