table_ngrams: Tabulate n-grams

In biogram: N-Gram Analysis of Biological Sequences

Description

Builds a contingency table of the n-gram counts versus their class labels.

Usage

table_ngrams(seq, ngrams, target)

Arguments

seq	vector or matrix describing sequence(s).
ngrams	vector of n-grams.
target	integer vector with target information (e.g. class labels). Must have at least two values.

Value

a data frame with the number of columns equal to the length of the target plus 1. The first column contains names of the n-grams. Further columns represents counts of n-grams for respective value of the target.

Examples

seqs_pos <- matrix(sample(c("a", "c", "g", "t"), 100, replace = TRUE, 
            prob = c(0.2, 0.4, 0.35, 0.05)), ncol = 5)
seqs_neg <- matrix(sample(c("a", "c", "g", "t"), 100, replace = TRUE), 
            ncol = 5)
tab <- table_ngrams(seq = rbind(seqs_pos, seqs_neg), 
                    ngrams = c("1_c.t_0", "1_g.g_0", "2_t.c_0", "2_g.g_0", "3_c.c_0", "3_g.c_0"), 
                    target = c(rep(1, 20), rep(0, 20)))
# see the results
print(tab)
# easily plot the results using ggplot2

biogram documentation built on March 31, 2020, 5:14 p.m.