gcTheoretical {ngsReports} | R Documentation

## Theoretical GC content

### Description

This object contains the theoretical GC content for each provided species, for both the genome and transcriptome, where available.

### Usage

    gcTheoretical

### Format

An object of class `TheoreticalGC` of length 1.

### Details

The object is defined with the S4 class `TheoreticalGC`. Species for which information is available can be found using the command `gcAvail(gcTheoretical)` and selecting the appropriate type.

Metadata is accessible using `mData(gcTheoretical)`.

All GC content was calculated using code from https://github.com/mikelove/fastqcTheoreticalGC using BSgenome packages. This provides a default set of GC content data for common organisms generated using 100bp reads/fragments and 1e6 reads.

### See Also

gcAvail

### Examples

    ## Check which genomes are included
    gcAvail(gcTheoretical, "Genome")

    ## Check which transcriptomes are included
    gcAvail(gcTheoretical, "Transcriptome")

[Package ngsReports version 1.2.0 Index]