codonUsage2df: Make codon usage data.frame

In jmw86069/splicejam: Analysis and Visualization of Gene Splice Variants and Transcriptome Data

Make codon usage data.frame

Description

Make codon usage data.frame

Usage

codonUsage2df(file, ...)

Arguments

file	path to the codon usage file

Details

This function imports a text file containing codon usage, and creates a data.frame with columns containing the codon, fraction, and count. The colname fraction represents the fraction observed counts per codon compared to the codon with the highest counts, for each amino acid. For example, an amino acid with only one codon would be c(1.0). An amino acid with two codons, with observed counts c(100, 200), would have fraction values c(0.5, 1.0).

The format is derived from published files, one example is included in the package extdata/Mouse_codon_usage.txt, which can be accessed using the command:

system.file("extdata", "Mouse_codon_usage.txt", package="farrisdata")

Value

data.frame containing codon usage data, with colnames codon, frequency, and count.

See Also

Other jam codon usage functions: dna2codon(), jamCai()

Examples

codonFile <- system.file("extdata", "Mouse_codon_usage.txt", package="splicejam");
codonDF <- codonUsage2df(codonFile);

jmw86069/splicejam documentation built on Nov. 4, 2024, 10:53 a.m.