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 |