Man pages for alakazam
Immunoglobulin Clonal Lineage and Diversity Analysis

ABBREV_AAAmino acid abbreviation translations
AbundanceCurve-classS4 class defining a clonal abundance curve
alakazamThe alakazam package
aliphaticCalculates the aliphatic index of amino acid sequences
aminoAcidPropertiesCalculates amino acid chemical properties for sequence data
baseThemeStandard ggplot settings
buildPhylipLineageInfer an Ig lineage using PHYLIP
bulkCalculates the average bulkiness of amino acid sequences
calcCoverageCalculate sample coverage
calcDiversityCalculate the diversity index
ChangeoClone-classS4 class defining a clone
chargeCalculates the net charge of amino acid sequences.
checkColumnsCheck data.frame for valid columns and issue message if...
collapseDuplicatesRemove duplicate DNA sequences and combine annotations
countClonesTabulates clones sizes
countGenesTabulates V(D)J allele, gene or family usage.
countPatternsCount sequence patterns
cpuCountAvailable CPU cores
DEFAULT_COLORSDefault colors
DiversityCurve-classS4 class defining a diversity curve
DiversityTest-classS4 class defining diversity significance
EdgeTest-classS4 class defining edge significance
estimateAbundanceEstimates the complete clonal relative abundance distribution
ExampleDbExample Change-O database
ExampleTreesExample Ig lineage trees
extractVRegionExtracts FWRs and CDRs from IMGT-gapped sequences
getAAMatrixBuild an AA distance matrix
getDNAMatrixBuild a DNA distance matrix
getMRCARetrieve the first non-root node of a lineage tree
getPathLengthsCalculate path lengths from the tree root
getSegmentGet Ig segment allele, gene and family names
gravyCalculates the hydrophobicity of amino acid sequences
gridPlotPlot multiple ggplot objects
groupGenesGroup sequences by gene assignment
IMGT_REGIONSIMGT V-segment regions
isValidAASeqValidate amino acid sequences
IUPAC_CODESIUPAC ambiguous characters
makeChangeoCloneGenerate a ChangeoClone object for lineage construction
makeTempDirCreate a temporary folder
maskSeqEndsMasks ragged leading and trailing edges of aligned DNA...
maskSeqGapsMasks gap characters in DNA sequences
MRCATest-classS4 class defining edge significance
nonsquareDistCalculate pairwise distances between sequences
padSeqEndsPads ragged ends of aligned DNA sequences
pairwiseDistCalculate pairwise distances between sequences
pairwiseEqualCalculate pairwise equivalence between sequences
permuteLabelsPermute the node labels of a tree
plotAbundanceCurvePlots a clonal abundance distribution
plotDiversityCurvePlot the results of rarefyDiversity
plotDiversityTestPlot the results of TestDiversity
plotEdgeTestPlot the results of an edge permutation test
plotMRCATestPlot the results of a founder permutation test
plotSubtreesPlots subtree statistics for multiple trees
polarCalculates the average polarity of amino acid sequences
progressBarStandard progress bar
rarefyDiversityGenerate a clonal diversity index curve
readChangeoDbRead a Change-O tab-delimited database file
seqDistCalculate distance between two sequences
seqEqualTest DNA sequences for equality.
sortGenesSort V(D)J genes
stoufferMetaWeighted meta-analysis of p-values via Stouffer's method
summarizeSubtreesGenerate subtree summary statistics for a tree
tableEdgesTabulate the number of edges between annotations within a...
testDiversityPairwise test of the diversity index
testEdgesTests for parent-child annotation enchrichment in lineage...
testMRCATests for MRCA annotation enrichment in lineage trees
translateDNATranslate nucleotide sequences to amino acids
translateStringsTranslate a vector of strings
writeChangeoDbWrite a Change-O tab-delimited database file
alakazam documentation built on Sept. 21, 2018, 6:26 p.m.