GetGC: Calculate GC content within window around loci from a 'txLoc'...

In mevers/RNAModR: Functional Analysis of RNA Modifications

Description

Calculate GC content within window around loci from a txLoc object. See 'Details'.

Usage

GetGC(txLoc, flank = 10)

Arguments

txLoc	A txLoc object.
flank	An integer scalar; see 'Details'.

Details

The function calculates the GC content within a window around every locus from a txLoc object. The window is defined by extending the position of every txLoc site upstream and downstream by flank nucleotides (if possible). This is the low-level function that gets called from within PlotGC. There is no guarantee that this function will be exported in future versions of RNAModR.

Value

A list of DataFrame objects, each with the following columns:

1. id: A character vector

2. GC_tx_region: A numeric vector

3. GC_window: A numeric vector

4. sequence_window: A DNAStringSet object

Author(s)

Maurits Evers, [e-mail]

mevers/RNAModR documentation built on Nov. 17, 2019, 9:11 a.m.