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 |