diff --git a/DESCRIPTION b/DESCRIPTION index f27979e..21e138e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,6 +18,7 @@ Imports: formula.tools, GenomeInfoDb, GenomicAlignments, + GenomicFeatures, GenomicRanges (>= 1.37.16), ggplot2 (>= 2.2.0), gtools, diff --git a/NAMESPACE b/NAMESPACE index 0788b49..d835e37 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -105,6 +105,10 @@ importFrom(GenomeInfoDb,seqnames) importFrom(GenomeInfoDb,sortSeqlevels) importFrom(GenomicAlignments,qwidth) importFrom(GenomicAlignments,readGAlignments) +importFrom(GenomicFeatures,exons) +importFrom(GenomicFeatures,genes) +importFrom(GenomicFeatures,promoters) +importFrom(GenomicFeatures,transcripts) importFrom(GenomicRanges,GPos) importFrom(GenomicRanges,GRanges) importFrom(GenomicRanges,GRangesList) diff --git a/man/annotateCTSS.Rd b/man/annotateCTSS.Rd index 3573950..8d488d5 100644 --- a/man/annotateCTSS.Rd +++ b/man/annotateCTSS.Rd @@ -3,6 +3,7 @@ \name{annotateCTSS} \alias{annotateCTSS} \alias{annotateCTSS,CAGEexp,GRanges-method} +\alias{annotateCTSS,CAGEexp,TxDb-method} \alias{annotateTagClusters} \alias{annotateTagClusters,CAGEexp,GRanges-method} \alias{annotateConsensusClusters} @@ -13,6 +14,8 @@ annotateCTSS(object, ranges, upstream = 500, downstream = 500) \S4method{annotateCTSS}{CAGEexp,GRanges}(object, ranges, upstream = 500, downstream = 500) +\S4method{annotateCTSS}{CAGEexp,TxDb}(object, ranges) + annotateTagClusters(object, ranges, upstream = 500, downstream = 500) \S4method{annotateTagClusters}{CAGEexp,GRanges}(object, ranges, upstream = 500, downstream = 500) diff --git a/man/ranges2annot.Rd b/man/ranges2annot.Rd index 180c0ed..2c17910 100644 --- a/man/ranges2annot.Rd +++ b/man/ranges2annot.Rd @@ -2,9 +2,12 @@ % Please edit documentation in R/Annotations.R \name{ranges2annot} \alias{ranges2annot} +\alias{txdb2annot} \title{Hierarchical annotation of genomic regions.} \usage{ ranges2annot(ranges, annot, upstream = 500, downstream = 500) + +txdb2annot(ranges, annot) } \arguments{ \item{ranges}{A \code{\link[GenomicRanges:GRanges-class]{GenomicRanges::GRanges}} object, for example extracted from