get.gc.content {metaseqR} | R Documentation

## Return a named vector of GC-content for each genomic region

### Description

Returns a named numeric vector (names are the genomic region names, e.g. genes) given a data frame which can be converted to a GRanges object (e.g. it has at least chromosome, start, end fields). This function works best when the input annotation data frame has been retrieved using one of the SQL queries generated from `get.ucsc.query`, used in `get.ucsc.annotation`.

### Usage

        get.gc.content(ann, org)

### Arguments

`ann` | a data frame which can be converted to a GRanges object, that means it has at least the chromosome, start, end fields. Preferably, the output of `link{get.ucsc.annotation}`.
`org` | one of metaseqR supported organisms.

### Value

A named numeric vector.

### Author(s)

Panagiotis Moulos

### Examples

    ann <- get.ucsc.annotation("mm9","gene","ucsc")
    gc <- get.gc.content(ann,"mm9")

[Package metaseqR version 1.28.0 Index]