TheoreticalGC-class: The TheoreticalGC Object Class

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

The TheoreticalGC Object Class

Description

Contains Theoretical GC content for a selection of species

Details

Estimates are able to be retained for genomic and transcriptomic sequences. Values are stored as frequencies.

Value

An object of class TheoreticalGC

Slots

Genome

A data.frame containing theoretical GC content for genomic sequences

Transcriptome

A data.frame containing theoretical GC content for transcriptomic sequences

mData

A data.frame containing metadata about all species in the object

Examples

## How to form an object using your own fasta file
faDir <- system.file("extdata", package = "ngsReports")
faFile <- list.files(faDir, pattern = "fasta", full.names = TRUE)
gen_df <- estGcDistn(faFile, n = 200)
gen_df <- dplyr::rename(gen_df, Athaliana = Freq)
mData_df <-
    data.frame(Name = "Athaliana", Genome = TRUE, Transcriptome = FALSE)
tr_df <- data.frame()
myGC <- new(
   "TheoreticalGC", Genome = gen_df, Transcriptome = tr_df, mData = mData_df)

UofABioinformaticsHub/fastqcReports documentation built on April 1, 2024, 5:29 p.m.