appearance_to_binary {peptoolkit}

Transform Amino Acid Appearance Probability into -1, 0, or 1

Description

This function transforms the counts of amino acids to a -1, 0, 1 matrix based on a probability of appearance of each peptide in each position.

Usage

appearance_to_binary(x, threshold = 1.65, group = "Best", percentage = 0.05)

Arguments

x

A data frame containing peptide sequences.

threshold

The probability threshold to determine the transformation.

group

A character string indicating which part of the data to consider. Either 'Best' or 'Worst'.

percentage

The percentage of the data to consider, if group is specified.

Value

A matrix with the same dimensions as the input where each cell has been transformed to -1, 0, or 1 based on the probability threshold.

Examples

# Generate a mock data frame
peptide_data <- data.frame(Sequence = c("ACGT", "TGCA", "GATC", "CGAT"))

# Apply the function to the mock data
appearance_to_binary(peptide_data, group = "Best", percentage = 0.5)