Immunoglobulin Clonal Lineage and Diversity Analysis


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Documentation for package ‘alakazam’ version 0.2.3

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alakazam-package The alakazam package
ABBREV_AA Amino acid abbreviation translations
alakazam The alakazam package
aliphatic Calculates the aliphatic index of amino acid sequences
aminoAcidProperties Calculates amino acid chemical properties for sequence data
buildPhylipLineage Infer an Ig lineage using PHYLIP
bulk Calculates the average bulkiness of amino acid sequences
calcCoverage Calculate sample coverage
calcDiversity Calculate the diversity index
ChangeoClone S4 class defining a clone
ChangeoClone-class S4 class defining a clone
charge Calculates the net charge of amino acid sequences.
collapseDuplicates Remove duplicate DNA sequences and combine annotations
countClones Tabulates clones sizes
countGenes Tabulates V(D)J allele, gene or family usage.
countPatterns Count sequence patterns
DEFAULT_COLORS Default colors
DiversityCurve S4 class defining diversity curve
DiversityCurve-class S4 class defining diversity curve
DiversityTest S4 class defining diversity significance
DiversityTest-class S4 class defining diversity significance
DNA_COLORS Default colors
estimateAbundance Estimates the complete clonal relative abundance distribution
ExampleTrees Example Ig lineage trees
extractVRegion Extracts FWRs and CDRs from IMGT-gapped sequences
getAAMatrix Build an AA distance matrix
getAllele Get Ig segment allele, gene and family names
getDNAMatrix Build a DNA distance matrix
getFamily Get Ig segment allele, gene and family names
getGene Get Ig segment allele, gene and family names
getSegment Get Ig segment allele, gene and family names
getSeqDistance Calculate distance between two sequences
getSeqMatrix Calculate pairwise distances between sequences
gravy Calculates the hydrophobicity of amino acid sequences
IG_COLORS Default colors
IMGT_REGIONS IMGT V-segment regions
isValidAASeq Validate amino acid sequences
IUPAC_AA IUPAC ambiguous characters
IUPAC_CODES IUPAC ambiguous characters
IUPAC_DNA IUPAC ambiguous characters
makeChangeoClone Generate a ChangeoClone object for lineage construction
makeTempDir Create a temporary folder
maskSeqEnds Masks ragged leading and trailing edges of aligned DNA sequences
maskSeqGaps Masks gap characters in DNA sequences
multiggplot Plot multiple ggplot objects
plotAbundance Plots a clonal abundance distribution
plotDiversityCurve Plot the results of rarefyDiversity
polar Calculates the average polarity of amino acid sequences
print-method S4 class defining diversity curve
print-method S4 class defining diversity significance
rarefyDiversity Generate a clonal diversity index curve
readChangeoDb Read a Change-O tab-delimited database file
stoufferMeta Weighted meta-analysis of p-values via Stouffer's method
testDiversity Pairwise test of the diversity index
testSeqEqual Test DNA sequences for equality.
translateDNA Translate nucleotide sequences to amino acids
translateStrings Translate a vector of strings
TR_COLORS Default colors
writeChangeoDb Write a Change-O tab-delimited database file