GCcontent {biovizBase} | R Documentation

## GC content computation for BSgenome

### Description

Compute GC content in a certain region of a BSgenome object

### Usage

    GCcontent(obj, ..., view.width, as.prob = TRUE)

### Arguments

`obj` | BSgenome object
`...` | Arguments passed to getSeq method for BSgenome package.
`view.width` | Passed to `letterFrequencyInSlidingView`, the constant (e.g. 35, 48, 1000) size of the "window" to slide along `obj`. The specified `letters` are tabulated in each window of length `view.width`. The rows of the result (see value) correspond to the various windows.
`as.prob` | If TRUE return percentage of GC content, otherwise return counts.

### Details

GC content is an interesting variable may be related to various biological questions. So we need a way to compute GC content in a certain region of a reference genome. GCcontent function is a wrapper around getSeq function in BSgenome package and `letterFrequency`, `letterFrequencyInSlidingView` in Biostrings package.

if the `view.width` is specified, the GC content will be computed in the sliding view

### Value

Numeric value indicate count or percentage

### Author(s)

Tengfei Yin

### Examples

    library(BSgenome.Hsapiens.UCSC.hg19)
    GCcontent(Hsapiens, GRanges("chr1", IRanges(1e6, 1e6 + 1000)))

[Package biovizBase version 1.28.2 Index]