plotTSS: Plot TSSs and clusters

Description Usage Arguments Examples

Description

Plots Gviz-track of TSSs, clusters, and genes.

Usage

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plotTSS(object,samples,tssData = "processed",clusters = "assigned",
clusterThreshold = 0.02,genelist,Bidirection = TRUE,up.dis =500,down.dis = 500)

## S4 method for signature 'TSSr'
plotTSS(
  object,
  samples,
  tssData = "processed",
  clusters = "assigned",
  clusterThreshold = 0.02,
  genelist,
  Bidirection = TRUE,
  up.dis = 500,
  down.dis = 500
)

Arguments

object

A TSSr object.

samples

Specify samples to be included for plotting.

tssData

Specify which TSS data to be included for plotting: "raw" or "processed".

clusters

Specify which cluster data to be included for plotting: "all" or "assigned".

clusterThreshold

Ignore downstream clusters if signal < filterClusterThreshold*the strongest clusters within the same gene promoter region. Default value = 0.02.

genelist

List of gene names used for plotting.

Bidirection

Specify whether to display bidirectional TSS signals within defined region. Default is TRUE.

up.dis

Distance upstream of genes to specify plotting range. Default value = 500.

down.dis

Distance downstream of genes to specify plotting range. Default value = 500.

Examples

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plotTSS(exampleTSSr, samples=c("control","treat"), genelist=c("YBL017C","YBL067C")
,up.dis =500, down.dis = 500)

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