eventPlot {SPLINTER} | R Documentation |
eventPlot
eventPlot(transcripts, roi_plot = NULL, bams = c(), names = c(), annoLabel = c("Gene A"), rspan = 1000, pfam_dom = NULL, showAll = TRUE)
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 |
pfam_dom |
optional GRanges object of PFAM domains from UCSC Tables. |
showAll |
logical. TRUE = display splice junctions of entire view or FALSE = just roi. |
a Gviz plot of genomic region
Diana Low
# 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)