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Make codon usage data.frame

Source: R/jambio-tx.R
codonUsage2df.Rd

Make codon usage data.frame

Usage

codonUsage2df(file, ...)

Arguments

file

path to the codon usage file

Value

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

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")

See also

Other ALE and codon functions: ale2violin(), dna2codon(), getFirstStrandedFromGRL(), jamCai(), tx2ale()

Examples

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