PLOTc: PLOTc plot RNA-seq and ribo-seq together for one datasets.

View source: R/code.R

PLOTcR Documentation

PLOTc plot RNA-seq and ribo-seq together for one datasets.

Description

PLOTc plot RNA-seq and ribo-seq together for one datasets. It also contains a plot with transcript models.

Usage

PLOTc(
  YFG,
  RNAbam1 = RNAseqBam1,
  ribo1 = Ribo1,
  ylab1 = Ribolab1,
  SAMPLE1 = S_NAME1,
  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.

ribo1

riboseq dataset

SAMPLE1

name of sample 1

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

Value

Both RNAseq and Riboseq plot together for one set of data


hsinyenwu/RiboPlotR documentation built on Sept. 15, 2023, 12:29 a.m.