annoGR-class {ChIPpeakAnno} | R Documentation |
annoGR
An object of class annoGR
represents the annotation data could be
used by annotationPeakInBatch.
## S4 method for signature 'GRanges' annoGR(ranges, feature="group", date, ...) ## S4 method for signature 'TxDb' annoGR(ranges, feature=c( "gene", "transcript", "exon", "CDS", "fiveUTR", "threeUTR", "microRNA", "tRNAs", "geneModel"), date, source, mdata, OrganismDb) ## S4 method for signature 'EnsDb' annoGR(ranges, feature=c("gene", "transcript", "exon", "disjointExons"), date, source, mdata)
ranges |
|
feature |
annotation type |
date |
a Date object |
... |
could be following parameters |
source |
character, where the annotation comes from |
mdata |
data frame, metadata from annotation |
OrganismDb |
an object of OrganismDb. It is used for extracting gene symbol for geneModel group for TxDb |
Objects can be created by calls of the form
new("annoGR", date, elementMetadata, feature, mdata, ranges,
seqinfo, seqnames, source, strand)
slots inherit from GRanges. The ranges must have unique names.
source
character, where the annotation comes from
date
a Date object
feature
annotation type, could be "gene", "exon", "transcript", "CDS", "fiveUTR", "threeUTR", "microRNA", "tRNAs", "geneModel" for TxDb object, or "gene", "exon" "transcript" for EnsDb object
mdata
data frame, metadata from annotation
as(from, "annoGR"): Creates a annoGR object from a GRanges object.
as(from, "GRanges"): Create a GRanges object from a annoGR object.
Print basic info for annoGR object
Jianhong Ou
if(Sys.getenv("USER")=="jianhongou"){ library(EnsDb.Hsapiens.v79) anno <- annoGR(EnsDb.Hsapiens.v79) }