# Annotate clusters with GFF annotation file.

`annotateCluster.Rd`

Annotates clusters with gene or transcript names from GFF annotation file.

    annotateCluster(object,clusters = "consensusClusters",filterCluster = TRUE
    , filterClusterThreshold = 0.02, annotationType = "genes",upstream=1000
    , upstreamOverlap = 500,downstream = 0)

    # S4 method for TSSr
    annotateCluster(
      object,
      clusters = "consensusClusters",
      filterCluster = TRUE,
      filterClusterThreshold = 0.02,
      annotationType = "genes",
      upstream = 1000,
      upstreamOverlap = 500,
      downstream = 0
    )

## Arguments

object | A TSSr object
clusters | Clusters to be annotated: "consensusClusters" or "tagClusters". Default is "consensusClusters".
filterCluster | Logical indicating whether clusters downstream of a highly expressed cluster are filtered. Setting filterCluster as "TRUE" would reduce weak clusters brought from recapping, transcriptional or sequencing noise. Default is TRUE.
filterClusterThreshold | Ignore downstream clusters if signal < filterClusterThreshold*the strongest clusters within the same gene promoter region. Default value = 0.02.
annotationType | Specify annotation feature to be associated with: "gene" or "transcript". Default is "gene".
upstream | Upstream distance to the start position of annotation feature. Default value = 1000.
upstreamOverlap | Upstream distance to the start position of annotation feature if overlapped with the upstream neighboring feature. Default value = 500.
downstream | Downstream distance to the start position of annotation feature. Default value = 0. Note: if annotationType == "transctipt" or the gene annotations start from transcription start sites (TSSs), the recommended value = 500.

## Examples

    # \donttest{
    annotateCluster(exampleTSSr,clusters = "consensusClusters", filterCluster = TRUE
    , filterClusterThreshold = 0.02, annotationType = "genes", upstream=1000
    , upstreamOverlap = 500, downstream = 0)#>
    #> Annotating...#> Error in annotateCluster(exampleTSSr, clusters = "consensusClusters",     filterCluster = TRUE, filterClusterThreshold = 0.02, annotationType = "genes",     upstream = 1000, upstreamOverlap = 500, downstream = 0): Please provide correct refSource file!# }