biogram1.6.3 package

Add 1-grams

Coerce feature_test object to a data frame

Binarize

biogram - analysis of biological sequences using n-grams

Calculate value of criterion

Calculate Chi-squared-based measure

Calculate encoding distance

Calculate IG for single feature

Calculate KL divergence of features

Calculate partition index

Compute similarity index

Check chosen criterion

Clustering of sequences based on regular expression

Code n-grams

Construct and filter n-grams

Detect and count multiple n-grams in sequences

Count n-grams in sequences

Count specified n-grams

Count total number of n-grams

Create encoding

Create feature according to given contingency matrix

Get all possible n-Grams

criterion_distribution class

Categorize tested features

Decode n-grams

Degenerate protein sequence

Degenerate n-grams

Compute criterion distribution

Convert encoding to data frame

2d cross-tabulation

feature_test class

Convert encoding from full to simple format

Gap n-grams

Generate sequence

Generate single region

Generate single unigram

Generate unigrams

Get indices of n-grams

Validate n-gram

Convert letters to numbers

Convert list of sequences to matrix

Convert numbers to letters

n-grams to data frame

Plot criterion distribution

Position n-grams

Print tested features

Read FASTA files

Regenerate n-grams

regional_param class

Extract n-grams from sequence

Convert encoding from simple to full format

Summarize tested features

Tabulate n-grams

Permutation test for feature selection

Validate encoding

Write encodings to a file

Write FASTA files