plotSitesOnUTR: plotSitesOnUTR

Description Usage Arguments Value Examples

View source: R/getTranscriptSequence.R

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

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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

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

ETHZ-INS/scanMiRApp documentation built on Jan. 20, 2022, 5:51 p.m.