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Last data update: 2014.03.03

R: Plot histogram of distance from peak to nearest TSS

plot_dist_to_tss

R Documentation

Plot histogram of distance from peak to nearest TSS

Description

Create a histogram of the distance from each peak to the nearest transcription start site (TSS) of any gene.

Usage

plot_dist_to_tss(peaks, genome = "hg19")

Arguments

`peaks`	Either a data frame, a BED file, a .broadPeak file, or a .narrowPeak file. The data frame should have at least 3 columns: chrom, start, and end. Chrom should follow UCSC convention, e.g. "chrX". The file should be tab-delimited.
`genome`	A string indicating the genome upon which the peaks file is based. Supported genomes are listed by the `supported_genomes` function.

Value

A trellis plot object.

Author(s)

Ryan Welch welchr@umich.edu

Examples

library(chipenrich.data)
library(chipenrich)

# Create histogram of distance from peaks to nearest TSS.
data(peaks_E2F4)
plot_dist_to_tss(peaks_E2F4)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(chipenrich)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/chipenrich/plot_dist_to_tss.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot_dist_to_tss
> ### Title: Plot histogram of distance from peak to nearest TSS
> ### Aliases: plot_dist_to_tss
> 
> ### ** Examples
> 
> library(chipenrich.data)
> library(chipenrich)
> 
> # Create histogram of distance from peaks to nearest TSS.
> data(peaks_E2F4)
> plot_dist_to_tss(peaks_E2F4)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>