N-Gram Analysis of Biological Sequences

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Documentation for package ‘biogram’ version 1.6.3

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biogram-package biogram - analysis of biological sequences using n-grams
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 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