annotateCluster: Annotate clusters with GFF annotation file.

Description Usage Arguments Examples

Description

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

Usage

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

## S4 method for signature '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

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

Linlab-slu/TSSr documentation built on July 28, 2021, 12:59 a.m.