annotateCluster: Annotate clusters with GFF annotation file.

In Linlab-slu/TSSr: TSS sequencing data analysis

Annotate clusters with GFF annotation file.

Description

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

Usage

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: "genes" or "transcripts". Default is "genes".
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.

Value

Large List of elements - one element for each sample

Examples

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

Linlab-slu/TSSr documentation built on Oct. 23, 2024, 8:31 p.m.