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 |