df2ppm: Turn a data.frame with sequences into a positional...

In Ni-Ar/niar: Nice Interactive Analysis with R

Turn a data.frame with sequences into a positional probability matrix.

Description

Generates a positional probability matrix (PPM).

Usage

df2ppm(data, ID_col, alphabet, c = 5)

Arguments

data	A data.frame with a minimum of 2 columns. One named Sequence, the other named as you prefer that will be specified with ID_col.
ID_col	The name of the column in data to be used as the identifier of the Sequence column.
alphabet	A character vector containing the alphabet letters present in Sequence. Guessed by default.
c	an integer used to round up the numbers

Value

A data frame with positional probabilities.

Examples

df2ppm(data, ID_col = 'Species', alphabet = c("A", "C", "G", "T")) 

Ni-Ar/niar documentation built on Feb. 3, 2025, 9:25 a.m.