eventPlot: eventPlot

Description Usage Arguments Value Author(s) Examples

View source: R/main_splinter.R

Description

eventPlot

Usage

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eventPlot(transcripts, roi_plot = NULL, bams = c(), names = c(),
  annoLabel = c("Gene A"), rspan = 1000, showAll = TRUE)

Arguments

transcripts

GRanges object

roi_plot

GRanges object region to plot

bams

character vector of bam file locations

names

character vector of name labels

annoLabel

character. annotation label

rspan

integer or NULL. number of basepairs to span from roi. if NULL, will consider whole gene of roi

showAll

logical. TRUE = display splice junctions of entire view or FALSE = just roi.

Value

a Gviz plot of genomic region

Author(s)

Diana Low

Examples

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# define BAM files
data_path<-system.file("extdata",package="SPLINTER")
mt<-paste(data_path,"/mt_chr14.bam",sep="")
wt<-paste(data_path,"/wt_chr14.bam",sep="")

# plot results
eventPlot(transcripts=valid_tx,roi_plot=roi,bams=c(wt,mt),
 names=c('wt','mt'),rspan=1000)

SPLINTER documentation built on May 31, 2017, 2:54 p.m.

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