plotSitesOnUTR: plotSitesOnUTR

In ETHZ-INS/scanMiRApp: scanMiR shiny application

plotSitesOnUTR

Description

Wrapper function with minimal arguments to plot scanMiR-Binding sites on 3'UTRs of specified transcripts. The red dashed line indicates the background threshhold is indicated, the lightblue dashed line shows the average 8mer dissociation rate of the given miRNA

Usage

plotSitesOnUTR(
  tx,
  annotation,
  miRNA = NULL,
  label_6mers = FALSE,
  label_notes = FALSE,
  verbose = TRUE,
  ...
)

Arguments

tx	An ensembl TranscriptID
annotation	A ScanMiRAnno object.
miRNA	A miRNA name in the mirbase format (eg. "hsa-miR-485-5p"), a 'KdModel', or a miRNA sequence or target seed.
label_6mers	Logical whether to label 6mer sites in the plot
label_notes	Logical whether to label special sites in the plot (as TDMD or Slicing)
verbose	Logical; whether to print updates on the processing
...	Any further arguments passed to findSeedMatches

Value

Returns a ggplot.

Examples

anno <- ScanMiRAnno("fake")
plotSitesOnUTR( tx="ENSTFAKE0000056456", annotation=anno,
                miRNA="hsa-miR-155-5p" )

ETHZ-INS/scanMiRApp documentation built on March 16, 2024, 5:30 p.m.