PLOTch2: PLOTch2
In hsinyenwu/RiboPlotR: Plot Periodicity of Ribosome Profiling Data

PLOTch2

R Documentation

PLOTch2

Description

plot 2 sets of RNA-seq and ribo-seq for comparison. The max height for each plot is according to each sample (PLOTc2 is according to both). It also contains a plot with transcript models.

Usage

PLOTch2(
  YFG,
  RNAbam1 = RNAseqBam1,
  RNAbam2 = RNAseqBam2,
  ribo1 = Ribo1,
  ribo2 = Ribo2,
  SAMPLE1 = S_NAME1,
  SAMPLE2 = S_NAME2,
  CDSonly = FALSE,
  Extend = 50,
  isoform,
  uORF = NULL,
  NAME = "",
  uORFisoform
)

Arguments

`YFG`	Gene ID
`RNAbam1`	Dataset 1 to plot. Default is RNAseqBam1 that was loaded by rna_bam.ribo.
`RNAbam2`	Dataset 2 to plot. Default is RNAseqBam2 that was loaded by rna_bam.ribo.
`ribo1`	riboseq dataset 1
`ribo2`	riboseq dataset 2
`SAMPLE1`	name of sample 1
`SAMPLE2`	name of sample 2
`CDSonly`	TRUE or FALSE. Only plot CDS region or all riboseq reads in defined area. Default plot all riboseq reads in the defined area.
`Extend`	Integer. The number of extra nt ploted at the ends of the plots.
`isoform`	Integer. Which isoform to plot periodicity.
`uORF`	Gene ID for uORF
`NAME`	Name of the gene
`uORFisoform`	Isoform number of the uORF