biogram: N-Gram Analysis of Biological Sequences
Version 1.4

Tools for extraction and analysis of various n-grams (k-mers) derived from biological sequences (proteins or nucleic acids). Contains QuiPT (quick permutation test) for fast feature-filtering of the n-gram data.

AuthorMichal Burdukiewicz [cre, aut], Piotr Sobczyk [aut], Chris Lauber [aut]
Date of publication2017-01-06 01:18:55
MaintainerMichal Burdukiewicz <michalburdukiewicz@gmail.com>
LicenseGPL-3
Version1.4
URL https://github.com/michbur/biogram
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("biogram")

Getting started

Package overview
README.md
biogram package"

Popular man pages

calc_cs: Calculate Chi-squared-based measure
calc_kl: Calculate KL divergence of features
construct_ngrams: Construct and filter n-grams
count_ngrams: Count n-grams in sequences
count_specified: Count specified n-grams
encoding2df: Convert encoding to data frame
ngrams2df: n-grams to data frame
See all...

All man pages Function index File listing

Man pages

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
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
distr_crit: Compute criterion distribution
encoding2df: Convert encoding to data frame
fast_crosstable: Very fast 2d cross-tabulation
feature_test: feature_test class
gap_ngrams: Gap n-grams
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
seq2ngrams: Extract n-grams from sequence
summary.feature_test: Summarize tested features
table_ngrams: Tabulate n-grams
test_features: Permutation test for feature selection
validate_encoding: Validate encoding

Functions

aaprop Man page
add_1grams Man page Source code
add_1grams_positioned Source code
as.data.frame.feature_test Man page Source code
binarize Man page Source code
biogram Man page
biogram-package Man page
build_and_test Source code
calc_criterion Man page Source code
calc_cs Man page Source code
calc_ed Man page Source code
calc_ed_single Source code
calc_ig Man page Source code
calc_kl Man page Source code
calc_max_grams Source code
calc_occurences Source code
calc_pi Man page Source code
calc_pi_hidden Source code
calc_si Man page Source code
calc_si_hidden Source code
check_criterion Source code
cluster_reg_exp Man page Source code
code_ngrams Man page Source code
construct_ngrams Man page Source code
count_df Source code
count_multigrams Man page Source code
count_ngrams Man page Source code
count_ngrams_helper Source code
count_single_positioned_ngram Source code
count_single_unpositioned_ngram Source code
count_specified Man page Source code
count_total Man page Source code
create_criterion_distribution Source code
create_encoding Man page Source code
create_feature_target Man page Source code
create_feature_test Source code
create_merges Source code
create_ngrams Man page Source code
criterion_distribution Man page
cut.feature_test Man page Source code
decode_ngrams Man page Source code
decode_single_ngrams Source code
degenerate Man page Source code
distr_crit Man page Source code
encoding2df Man page Source code
encoding2matrix Source code
entlog Source code
fast_crosstable Man page Source code
feature_test Man page
gap_ngrams Man page Source code
gap_single_ngram Source code
get_ngrams_ind Man page Source code
human_cleave Man page
is_ngram Man page Source code
join_reg_exp Source code
l2n Man page Source code
list2matrix Man page Source code
n2l Man page Source code
ngrams2df Man page Source code
plot.criterion_distribution Man page Source code
position_ngrams Man page Source code
print.feature_test Man page Source code
reg_exp_df Source code
seq2ngrams Man page Source code
seq2ngrams_helper Source code
summary.feature_test Man page Source code
table_ngrams Man page Source code
test_features Man page Source code
validate_encoding Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/overview.R
inst/doc/overview.html
inst/doc/overview.Rmd
tests
tests/testthat
tests/testthat/test_create_ngrams.R
tests/testthat/test_table_ngrams.R
tests/testthat/test_crosstable.R
tests/testthat/test_position_ngrams.R
tests/testthat/test_seq2grams.R
tests/testthat/test_is_ngram.R
tests/testthat/test_quipt_consistency.R
tests/testthat/test_count_ngrams.R
tests/testthat/test_calc_ed.R
tests/testthat/test_get_ngrams_pos.R
tests/test-all.R
NAMESPACE
CHANGELOG
data
data/human_cleave.rda
data/aaprop.rda
R
R/count_ngrams.R
R/create_encoding.R
R/indices_and_positions.R
R/position_ngrams.R
R/test_features.R
R/calc_ed.R
R/human_cleave.R
R/table_ngrams.R
R/information_gain.R
R/seq2matrix.R
R/count_specified.R
R/utilities.R
R/aaprop.R
R/ngram_coding.R
R/criterion_distribution.R
R/kl_divergence.R
R/feature_test_class.R
R/construct_ngrams.R
R/criterions.R
R/biogram.R
R/distr_crit.R
R/add_remove_ngrams.R
R/calc_si.R
R/cluster_reg_exp.R
R/count_multigrams.R
R/data_manipulation.R
R/is_ngram.R
R/chi_square.R
R/degenerate.R
R/ngrams.R
vignettes
vignettes/biogram_pub.bib
vignettes/overview.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/calc_ed.Rd
man/create_feature_target.Rd
man/create_encoding.Rd
man/list2matrix.Rd
man/table_ngrams.Rd
man/get_ngrams_ind.Rd
man/seq2ngrams.Rd
man/calc_ig.Rd
man/cluster_reg_exp.Rd
man/calc_cs.Rd
man/degenerate.Rd
man/count_total.Rd
man/count_multigrams.Rd
man/calc_pi.Rd
man/plot.criterion_distribution.Rd
man/as.data.frame.feature_test.Rd
man/calc_criterion.Rd
man/binarize.Rd
man/position_ngrams.Rd
man/summary.feature_test.Rd
man/is_ngram.Rd
man/calc_si.Rd
man/construct_ngrams.Rd
man/fast_crosstable.Rd
man/cut.feature_test.Rd
man/count_specified.Rd
man/human_cleave.Rd
man/create_ngrams.Rd
man/calc_kl.Rd
man/gap_ngrams.Rd
man/code_ngrams.Rd
man/criterion_distribution.Rd
man/validate_encoding.Rd
man/count_ngrams.Rd
man/l2n.Rd
man/print.feature_test.Rd
man/encoding2df.Rd
man/test_features.Rd
man/decode_ngrams.Rd
man/feature_test.Rd
man/biogram-package.Rd
man/add_1grams.Rd
man/ngrams2df.Rd
man/n2l.Rd
man/aaprop.Rd
man/distr_crit.Rd
biogram documentation built on May 20, 2017, 3:56 a.m.

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