⚠️There's a newer version (1.4.2) of this package.Take me there.

alakazam (version 0.2.2)

Immunoglobulin Clonal Lineage and Diversity Analysis

Description

Core functionality, lineage reconstruction, and diversity analysis, and amino acid property analysis components of the Change-O tool suite.

Copy Link

Version

Install

install.packages('alakazam')

Monthly Downloads

1,626

Version

0.2.2

License

CC BY-NC-SA 4.0

Maintainer

Jason Vander Heiden

Last Published

January 29th, 2016

Functions in alakazam (0.2.2)

ExampleTrees

Example Ig lineage trees

charge

Calculates the net charge of amino acid sequences.

polar

Calculates the average polarity of amino acid sequences

DiversityTest-class

S4 class defining diversity significance

maskSeqEnds

Masks ragged leading and trailing edges of aligned DNA sequences

translateStrings

Translate a vector of strings

aminoAcidProperties

Calculates amino acid chemical properties for sequence data

testDiversity

Pairwise test of the diversity index

getDNAMatrix

Build a DNA distance matrix

maskSeqGaps

Masks gap characters in DNA sequences

IMGT_REGIONS

IMGT V-segment regions

readChangeoDb

Read a Change-O tab-delimited database file

makeTempDir

Create a temporary folder

multiggplot

Plot multiple ggplot objects

getSeqDistance

Calculate distance between two sequences

getAAMatrix

Build an AA distance matrix

countPatterns

Count sequence patterns

getSegment

Get Ig segment allele, gene and family names

countGenes

Tabulates V(D)J allele, gene or family usage.

plotAbundance

Plots a clonal abundance distribution

calcCoverage

Calculate sample coverage

plotDiversityCurve

Plot the results of rarefyDiversity

calcDiversity

Calculate the diversity index

rarefyDiversity

Generate a clonal diversity index curve

translateDNA

Translate nucleotide sequences to amino acids

DEFAULT_COLORS

Default colors

ChangeoClone-class

S4 class defining a clone

gravy

Calculates the hydrophobicity of amino acid sequences

makeChangeoClone

Generate a ChangeoClone object for lineage construction

isValidAASeq

Validate amino acid sequences

countClones

Tabulates clones sizes

extractVRegion

Extracts FWRs and CDRs from IMGT-gapped sequences

writeChangeoDb

Write a Change-O tab-delimited database file

estimateAbundance

Estimates the complete clonal relative abundance distribution

buildPhylipLineage

Infer an Ig lineage using PHYLIP

DiversityCurve-class

S4 class defining diversity curve

alakazam

The alakazam package

IUPAC_CODES

IUPAC ambiguous characters

ABBREV_AA

Amino acid abbreviation translations

collapseDuplicates

Remove duplicate DNA sequences and combine annotations

testSeqEqual

Test DNA sequences for equality.

getSeqMatrix

Calculate pairwise distances between sequences

bulk

Calculates the average bulkiness of amino acid sequences

stoufferMeta

Weighted meta-analysis of p-values via Stouffer's method

aliphatic

Calculates the aliphatic index of amino acid sequences