plotTSS: Plot TSSs and clusters

In Linlab-slu/TSSr: TSS sequencing data analysis

Plot TSSs and clusters

Description

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

Usage

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

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

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.
yFixed	Logical, specify whether to fix y axis limits. Default is TRUE.

Value

TSS and cluster examples visualized in a graph

Examples

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

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