gcTheoretical: Theoretical GC content

In UofABioinformaticsHub/fastqcReports: Load FastqQC reports and other NGS related files

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")

UofABioinformaticsHub/fastqcReports documentation built on July 23, 2024, 3:26 p.m.