rna_bam.ribo: Function to get bam file path, ribo-seq p-site information...

In hsinyenwu/RiboPlotR: Plot Periodicity of Ribosome Profiling Data

Function to get bam file path, ribo-seq p-site information and axis labels information.

Description

This function obtains the RNA-seq bam file path, ribo-seq p-site file information, and the labels for y axes of the RNA-seq and ribo-seq plots

Usage

rna_bam.ribo(
  Ribo1,
  Ribo2 = NULL,
  RNAseqBam1,
  RNAseqBam2 = NULL,
  RNAlab1 = "RNA_sample1",
  RNAlab2 = NULL,
  RNAseqBamPaired = "paired",
  Ribolab1 = "Ribo_sample1",
  Ribolab2 = NULL,
  S_NAME1 = "sample1",
  S_NAME2 = NULL,
  RNAbackground = "#FEFEAE"
)

Arguments

Ribo1	The first ribo-seq tsv file path.
Ribo2	The second ribo-seq tsv file path.
RNAseqBam1	The first RNA-seq bam file path.
RNAseqBam2	The second RNA-seq bam file path.
RNAlab1	The y-axis label for the first RNA-seq datasets.
RNAlab2	The y-axis label for the second RNA-seq datasets.
RNAseqBamPaired	Whether the RNA bam is paired-end. Enter "single" for single-end bam file. "paired" for paired-end bam file (default).
Ribolab1	The y-axis label for the first ribo-seq datasets.
Ribolab2	The y-axis label for the second ribo-seq datasets.
S_NAME1	Sample 1 name
S_NAME2	Sample 2 name
RNAbackground	The background color for RNA-seq results

Value

Assign pathes or tsv files to global environment required for downstream analysis

Examples

## Not run: 
uorf.structure(uorf_annotation="/Volumes/BACKUP/project2/TAIR10.29.gtf",dataSource="Araport",organism="Arabidopsis thaliana")

## End(Not run)

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