All functions

aaprop

Normalized amino acids properties

add_1grams()

Add 1-grams

as.data.frame(<feature_test>)

Coerce feature_test object to a data frame

binarize()

Binarize

biogram-package

biogram - analysis of biological sequences using n-grams

calc_criterion()

Calculate value of criterion

calc_cs()

Calculate Chi-squared-based measure

calc_ed()

Calculate encoding distance

calc_ig()

Calculate IG for single feature

calc_kl()

Calculate KL divergence of features

calc_pi()

Calculate partition index

calc_si()

Compute similarity index

check_criterion()

Check chosen criterion

cluster_reg_exp()

Clustering of sequences based on regular expression

code_ngrams()

Code n-grams

construct_ngrams()

Construct and filter n-grams

count_multigrams()

Detect and count multiple n-grams in sequences

count_ngrams()

Count n-grams in sequences

count_specified()

Count specified n-grams

count_total()

Count total number of n-grams

create_encoding()

Create encoding

create_feature_target()

Create feature according to given contingency matrix

create_ngrams()

Get all possible n-Grams

criterion_distribution

criterion_distribution class

cut(<feature_test>)

Categorize tested features

decode_ngrams()

Decode n-grams

degenerate()

Degenerate protein sequence

degenerate_ngrams()

Degenerate n-grams

distr_crit()

Compute criterion distribution

encoding2df()

Convert encoding to data frame

fast_crosstable()

2d cross-tabulation

feature_test

feature_test class

full2simple()

Convert encoding from full to simple format

gap_ngrams()

Gap n-grams

generate_sequence()

Generate sequence

generate_single_region()

Generate single region

generate_single_unigram()

Generate single unigram

generate_unigrams()

Generate unigrams

get_ngrams_ind()

Get indices of n-grams

human_cleave

Human signal peptides cleavage sites

is_ngram()

Validate n-gram

l2n()

Convert letters to numbers

list2matrix()

Convert list of sequences to matrix

n2l()

Convert numbers to letters

ngrams2df()

n-grams to data frame

plot(<criterion_distribution>)

Plot criterion distribution

position_ngrams()

Position n-grams

print(<feature_test>)

Print tested features

read_fasta()

Read FASTA files

regenerate()

Regenerate n-grams

regional_param

regional_param class

seq2ngrams()

Extract n-grams from sequence

simple2full()

Convert encoding from simple to full format

summary(<feature_test>)

Summarize tested features

table_ngrams()

Tabulate n-grams

test_features()

Permutation test for feature selection

validate_encoding()

Validate encoding

write_encoding()

Write encodings to a file

write_fasta()

Write FASTA files