Immunoglobulin Clonal Lineage and Diversity Analysis


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Documentation for package ‘alakazam’ version 0.2.11

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alakazam-package The alakazam package
ABBREV_AA Amino acid abbreviation translations
AbundanceCurve S4 class defining a clonal abundance curve
AbundanceCurve-class S4 class defining a clonal abundance curve
AbundanceCurve-method S4 class defining a clonal abundance curve
alakazam The alakazam package
aliphatic Calculates the aliphatic index of amino acid sequences
aminoAcidProperties Calculates amino acid chemical properties for sequence data
baseTheme Standard ggplot settings
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.
checkColumns Check data.frame for valid columns and issue message if invalid
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
cpuCount Available CPU cores
DEFAULT_COLORS Default colors
DiversityCurve S4 class defining a diversity curve
DiversityCurve-class S4 class defining a diversity curve
DiversityCurve-method S4 class defining a diversity curve
DiversityTest S4 class defining diversity significance
DiversityTest-class S4 class defining diversity significance
DiversityTest-method S4 class defining diversity significance
DNA_COLORS Default colors
EdgeTest S4 class defining edge significance
EdgeTest-class S4 class defining edge significance
EdgeTest-method S4 class defining edge significance
estimateAbundance Estimates the complete clonal relative abundance distribution
ExampleDb Example Change-O database
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
getMRCA Retrieve the first non-root node of a lineage tree
getPathLengths Calculate path lengths from the tree root
getSegment Get Ig segment allele, gene and family names
gravy Calculates the hydrophobicity of amino acid sequences
gridPlot Plot multiple ggplot objects
groupGenes Group sequences by gene assignment
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
MRCATest S4 class defining edge significance
MRCATest-class S4 class defining edge significance
MRCATest-method S4 class defining edge significance
nonsquareDist Calculate pairwise distances between sequences
padSeqEnds Pads ragged ends of aligned DNA sequences
pairwiseDist Calculate pairwise distances between sequences
pairwiseEqual Calculate pairwise equivalence between sequences
permuteLabels Permute the node labels of a tree
plot-method S4 class defining a clonal abundance curve
plot-method S4 class defining a diversity curve
plot-method S4 class defining diversity significance
plot-method S4 class defining edge significance
plot-method S4 class defining edge significance
plotAbundanceCurve Plots a clonal abundance distribution
plotDiversityCurve Plot the results of rarefyDiversity
plotDiversityTest Plot the results of TestDiversity
plotEdgeTest Plot the results of an edge permutation test
plotMRCATest Plot the results of a founder permutation test
plotSubtrees Plots subtree statistics for multiple trees
polar Calculates the average polarity of amino acid sequences
print-method S4 class defining a clonal abundance curve
print-method S4 class defining a diversity curve
print-method S4 class defining diversity significance
print-method S4 class defining edge significance
print-method S4 class defining edge significance
progressBar Standard progress bar
rarefyDiversity Generate a clonal diversity index curve
readChangeoDb Read a Change-O tab-delimited database file
seqDist Calculate distance between two sequences
seqEqual Test DNA sequences for equality.
sortGenes Sort V(D)J genes
stoufferMeta Weighted meta-analysis of p-values via Stouffer's method
summarizeSubtrees Generate subtree summary statistics for a tree
tableEdges Tabulate the number of edges between annotations within a lineage tree
testDiversity Pairwise test of the diversity index
testEdges Tests for parent-child annotation enchrichment in lineage trees
testMRCA Tests for MRCA annotation enrichment in lineage trees
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