gcContentCalc

gcContentCalc,GRanges,BSgenome-method

gcContentCalc,data.frame,BSgenome-method

A <code>GRanges</code> object or a <code>data.frame</code>, with columns <code>chr</code>
           and either <code>position</code> or <code>start</code>, <code>end</code> and <code>strand</code>.

Bases around the locations that are in the window. Calculation will
                consider <code>windowSize/2</code> bases upstream, and <code>windowSize / 2 - 1 </code>
                bases downstream.

window

The <code>BSgenome</code> object to calculate gcContent upon.

organism

Whether to print the progess of processing.

verbose

The <code>verbose</code> variable for the <code>data.frame</code> method,
             passed onto the <code>GRanges</code> method.

Function to calculate the GC content of windows

Tools for the analysis of enrichment-based epigenomic
data.  Features include summarization and visualization of
epigenomic data across promoters according to gene expression
context, finding regions of differential methylation/binding,
BayMeth for quantifying methylation etc.

Mark Robinson

Repitools

Epigenomic tools

gcContentCalc function

A <code>GRanges</code> object or a <code>data.frame</code>, with columns <code>chr</code>
           and either <code>position</code> or <code>start</code>, <code>end</code> and <code>strand</code>.

Bases around the locations that are in the window. Calculation will
                consider <code>windowSize/2</code> bases upstream, and <code>windowSize / 2 - 1</code>
                bases downstream.

The <code>verbose</code> variable for the <code>data.frame</code> method,
             passed onto the <code>GRanges</code> method.

gcContentCalc: Calculate The gcContent of a Region

Description

Usage

Arguments

Value

Details

Examples