Plot TSSs and clusters

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

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

# S4 method for 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

# \donttest{
plotTSS(exampleTSSr, samples=c("control","treat"), genelist=c("YBL017C","YBL067C")
,up.dis =500, down.dis = 500)
#> Plotting TSS graphs...
#> Import genomic features from the file as a GRanges object ... 
#> Error in open.connection(con, open): cannot open the connection
# }