DJEplotSplice: DJEplotSplice: Differential junction usage plot

In MauerLab/DJExpress: An integrated application for differential splicing analysis and visualization

Description

Plots relative log-fold changes by junctions for the specified gene and highlights the significantly spliced junctions. This is a wrapper function of limma plotSplice.

Usage

DJEplotSplice(
  analize.out,
  geneID = NULL,
  gtf = NULL,
  target.junction = NULL,
  genecolname = NULL,
  rank = 1L,
  logFC = 2,
  meanExp = 10,
  FDR = 0.05
)

Arguments

analize.out	output object from DJEanalyze()
geneID	gene name for which plot is generated
gtf	Reference transcriptome in genecode gtf file format. Used to define gene coordinates
target.junction	Junction IDs to highlight within gene model plot. Maximum 5 junctions.
genecolname	column name of fit$genes containing gene IDs. Defaults to fit$genecolname
rank	integer, if geneid=NULL then this ranked gene will be plotted
logFC	numeric: log2-fold-change value cutoff in junction usage to define significance in plot
meanExp	numeric: mean expression value cutoff in tested condition group to define significance in plot
FDR	numeric: adjusted p-value cutoff in the linear model fit to define significance

Value

interactive highcharts plot showing relative logFC across junctions in target gene

Examples

data(DJEanlz)
iPlot.out <- DJEplotSplice(DJEanlz, geneID="ENAH", logFC = 0.8, FDR = 0.05)

MauerLab/DJExpress documentation built on Jan. 1, 2022, 12:57 p.m.