shazam: Immunoglobulin Somatic Hypermutation Analysis
Version 0.1.7

Provides a computational framework for Bayesian estimation of antigen-driven selection in immunoglobulin (Ig) sequences, providing an intuitive means of analyzing selection by quantifying the degree of selective pressure. Also provides tools to profile mutations in Ig sequences, build models of somatic hypermutation (SHM) in Ig sequences, and make model-dependent distance comparisons of Ig repertoires.

AuthorMohamed Uduman [aut], Gur Yaari [aut], Namita Gupta [aut], Jason Vander Heiden [aut, cre], Ang Cui [ctb], Susanna Marquez [ctb], Julian Zhou [ctb], Nima Nouri [ctb], Steven Kleinstein [aut, cph]
Date of publication2017-05-14 20:44:48 UTC
MaintainerJason Vander Heiden <jason.vanderheiden@yale.edu>
LicenseCC BY-SA 4.0
Version0.1.7
URL http://shazam.readthedocs.io
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("shazam")

Getting started

README.md
Shazam: Inferring SHM targeting models
Shazam: Mutation analysis
Shazam: Quantification of selection pressure
Shazam: Tuning clonal assignment thresholds with nearest neighbor distances

Popular man pages

createMutationDefinition: Creates a MutationDefinition
editBaseline: Edit the Baseline object
HKL_S5F: Human kappa and lambda light chain, silent, 5-mer, functional...
MK_RS1NF: Mouse kappa chain, replacement and silent, 1-mer,...
MutationDefinition-class: S4 class defining replacement and silent mutation definitions
MUTATION_SCHEMES: Amino acid mutation definitions
observedMutations: Calculate observed numbers of mutations
See all...

All man pages Function index File listing

Man pages

Baseline-class: S4 class defining a BASELINe (selection) object
calcBaseline: Calculate the BASELINe PDFs
calcExpectedMutations: Calculate expected mutation frequencies of a sequence
calcObservedMutations: Count the number of observed mutations in a sequence.
calcTargetingDistance: Calculates a 5-mer distance matrix from a TargetingModel...
clearConsole: Clears the console
collapseClones: Constructs effective clonal sequences
createBaseline: Creates a Baseline object
createMutabilityMatrix: Builds a mutability model
createMutationDefinition: Creates a MutationDefinition
createRegionDefinition: Creates a RegionDefinition
createSubstitutionMatrix: Builds a substitution model
createTargetingMatrix: Calculates a targeting rate matrix
createTargetingModel: Creates a TargetingModel
DensityThreshold-class: Output of the 'dens' method of findThreshold
distToNearest: Distance to nearest neighbor
editBaseline: Edit the Baseline object
expectedMutations: Calculate expected mutation frequencies
extendMutabilityMatrix: Extends a mutability model to include Ns.
extendSubstitutionMatrix: Extends a substitution model to include Ns.
findThreshold: Find distance threshold
getBaselineStats: Gets the summary statistics of a Baseline object
getnproc: Determines the numbers of CPU cores available
getPlatform: Determines the OS platform being used
GmmThreshold-class: Output of the 'gmm' method of findThreshold
groupBaseline: Group BASELINe PDFs
HH_S1F: Human heavy chain, silent, 1-mer, functional substitution...
HH_S5F: Human heavy chain, silent, 5-mer, functional targeting model.
HKL_S1F: Human kappa and lambda chain, silent, 1-mer, functional...
HKL_S5F: Human kappa and lambda light chain, silent, 5-mer, functional...
IMGT_SCHEMES: IMGT unique numbering schemes
makeAverage1merMut: Make a 1-mer mutability model by averaging over a 5-mer...
makeAverage1merSub: Make a 1-mer substitution model by averaging over a 5-mer...
makeDegenerate5merMut: Make a degenerate 5-mer mutability model based on a 1-mer...
makeDegenerate5merSub: Make a degenerate 5-mer substitution model based on a 1-mer...
minNumMutationsTune: Parameter tuning for minNumMutations
minNumSeqMutationsTune: Parameter tuning for minNumSeqMutations
MK_RS1NF: Mouse kappa chain, replacement and silent, 1-mer,...
MK_RS5NF: Mouse kappa light chain, replacement and silent, 5-mer,...
MutationDefinition-class: S4 class defining replacement and silent mutation definitions
MUTATION_SCHEMES: Amino acid mutation definitions
observedMutations: Calculate observed numbers of mutations
plotBaselineDensity: Plots BASELINe probability density functions
plotBaselineSummary: Plots BASELINe summary statistics
plotDensityThreshold: Plot findThreshold results for the density method
plotGmmThreshold: Plot findThreshold results for the gmm method
plotMutability: Plot mutability probabilities
plotTune: Visualize parameter tuning for minNumMutations and...
RegionDefinition-class: S4 class defining a region definition
shazam: The shazam package
shmulateSeq: Simulate mutations in a single sequence
shmulateTree: Simulate mutations in a lineage tree
slideWindowDb: Sliding window approach towards filtering sequences in a...
slideWindowSeq: Sliding window approach towards filtering a single sequence
slideWindowTune: Parameter tuning for sliding window approach
slideWindowTunePlot: Visualize parameter tuning for sliding window approach
summarizeBaseline: Calculate BASELINe summary statistics
TargetingModel-class: S4 class defining a targeting model
testBaseline: Two-sided test of BASELINe PDFs
U5N: Uniform 5-mer null targeting model.
writeTargetingDistance: Write targeting model distances to a file

Functions

Baseline Man page
Baseline-class Man page
CHARGE_MUTATIONS Man page
DensityThreshold Man page
DensityThreshold-class Man page
DensityThreshold-method Man page Man page
GmmThreshold Man page
GmmThreshold-class Man page
GmmThreshold-method Man page Man page
HH_S1F Man page
HH_S5F Man page
HKL_S1F Man page
HKL_S5F Man page
HYDROPATHY_MUTATIONS Man page
IMGT_SCHEMES Man page
IMGT_V Man page
IMGT_V_BY_REGIONS Man page
MK_RS1NF Man page
MK_RS5NF Man page
MUTATION_SCHEMES Man page
MutationDefinition Man page
MutationDefinition-class Man page
POLARITY_MUTATIONS Man page
PowersOfTwo Source code
RegionDefinition Man page
RegionDefinition-class Man page
TargetingModel Man page
TargetingModel-class Man page
U5N Man page
VOLUME_MUTATIONS Man page
allCodonMuts Source code
allValidChars Source code
analyzeMutations2NucUri Source code
baseline2DistPValue Source code
baselineCI Source code
baselinePValue Source code
baselineSigma Source code
binMutationsByRegion Source code
break2chunks Source code
calcBaseline Man page Source code
calcBaselineBinomialPdf Source code
calcBaselineHelper Source code
calcClonalConsensus Source code
calcExpectedMutations Man page Source code
calcObservedMutations Man page Source code
calcTargetingDistance Man page Source code
calculateMutationalPaths Source code
calculateTargeting Source code
calculate_bayesGHelper Source code
canMutateTo Source code
checkColumns Source code
clearConsole Man page Source code
collapseClones Man page Source code
collapseMatrixToVector Source code
combineWeightedPosteriors Source code
computeCodonTable Source code
computeMutationTypes Source code
convolutionPowersOfTwo Source code
convolutionPowersOfTwoByTwos Source code
createBaseline Man page Source code
createMutabilityMatrix Man page Source code
createMutationDefinition Man page Source code
createRegionDefinition Man page Source code
createSubstitutionMatrix Man page Source code
createTargetingMatrix Man page Source code
createTargetingModel Man page Source code
dist5Mers Source code
distToNearest Man page Source code
doparProgressBar Source code
editBaseline Man page Source code
expectedMutations Man page Source code
extendMutabilityMatrix Man page Source code
extendSubstitutionMatrix Man page Source code
fastConv Source code
findThreshold Man page Source code
findUniqSeq Source code
getBaseTheme Source code
getBaselineStats Man page Source code
getCharsInModel Source code
getCodonNucs Source code
getCodonNumb Source code
getCodonPos Source code
getContextInCodon Source code
getPlatform Man page Source code
getnproc Man page Source code
gmmFit Source code
gmmThreshold Source code
groupBaseline Man page Source code
groupPosteriors Source code
listMutations Source code
listObservedMutations Source code
makeAverage1merMut Man page Source code
makeAverage1merSub Man page Source code
makeDegenerate5merMut Man page Source code
makeDegenerate5merSub Man page Source code
makeNullRegionDefinition Source code
makeTargetingTestDb Source code
minNumMutationsTune Man page Source code
minNumSeqMutationsTune Man page Source code
mutationType Source code
mutationTypeOptimized Source code
nGaussianArea Source code
nearestDist Source code
observedMutations Man page Source code
pairwise5MerDist Source code
plot,DensityThreshold,missing-method Man page
plot,GmmThreshold,missing-method Man page
plotBaselineDensity Man page Source code
plotBaselineSummary Man page Source code
plotDensityThreshold Man page Source code
plotGmmThreshold Man page Source code
plotMutability Man page Source code
plotTune Man page Source code
print,DensityThreshold-method Man page
print,GmmThreshold-method Man page
removeCodonGaps Source code
rescaleMutability Source code
sampleMut Source code
shazam Man page
shazam-package Man page
shmulateSeq Man page Source code
shmulateTree Man page Source code
slideWindowDb Man page Source code
slideWindowSeq Man page Source code
slideWindowSeqHelper Source code
slideWindowTune Man page Source code
slideWindowTunePlot Man page Source code
smoothValley Source code
summarizeBaseline Man page Source code
symmetrize Source code
testBaseline Man page Source code
toupperColumns Source code
translateCodonToAminoAcid Source code
weighted_conv Source code
window5Mers Source code
writeTargetingDistance Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/Baseline-Vignette.R
inst/doc/DistToNearest-Vignette.pdf
inst/doc/Baseline-Vignette.pdf
inst/doc/DistToNearest-Vignette.Rmd
inst/doc/Targeting-Vignette.Rmd
inst/doc/DistToNearest-Vignette.R
inst/doc/Mutation-Vignette.pdf
inst/doc/Mutation-Vignette.Rmd
inst/doc/Targeting-Vignette.R
inst/doc/Targeting-Vignette.pdf
inst/doc/Mutation-Vignette.R
inst/doc/Baseline-Vignette.Rmd
inst/markr
inst/markr/build.R
NAMESPACE
NEWS.md
data
data/HH_S1F.rda
data/VOLUME_MUTATIONS.rda
data/HYDROPATHY_MUTATIONS.rda
data/HH_S5F.rda
data/MK_RS1NF.rda
data/CHARGE_MUTATIONS.rda
data/POLARITY_MUTATIONS.rda
data/HKL_S1F.rda
data/IMGT_V_BY_REGIONS.rda
data/IMGT_V.rda
data/HKL_S5F.rda
data/U5N.rda
data/MK_RS5NF.rda
R
R/DistToNearest.R
R/Core.R
R/Shmulate.R
R/sysdata.rda
R/Baseline.R
R/Shazam.R
R/TargetingModels.R
R/RegionDefinitions.R
R/MutationDefinitions.R
R/MutationProfiling.R
vignettes
vignettes/DistToNearest-Vignette.Rmd
vignettes/Targeting-Vignette.Rmd
vignettes/Mutation-Vignette.Rmd
vignettes/Baseline-Vignette.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/HKL_S5F.Rd
man/HH_S5F.Rd
man/clearConsole.Rd
man/HH_S1F.Rd
man/Baseline-class.Rd
man/DensityThreshold-class.Rd
man/shmulateTree.Rd
man/plotDensityThreshold.Rd
man/TargetingModel-class.Rd
man/createMutationDefinition.Rd
man/calcExpectedMutations.Rd
man/plotMutability.Rd
man/editBaseline.Rd
man/shazam.Rd
man/slideWindowDb.Rd
man/RegionDefinition-class.Rd
man/slideWindowTunePlot.Rd
man/summarizeBaseline.Rd
man/calcBaseline.Rd
man/plotBaselineDensity.Rd
man/createBaseline.Rd
man/IMGT_SCHEMES.Rd
man/plotTune.Rd
man/getnproc.Rd
man/testBaseline.Rd
man/makeDegenerate5merSub.Rd
man/createTargetingMatrix.Rd
man/MUTATION_SCHEMES.Rd
man/slideWindowTune.Rd
man/groupBaseline.Rd
man/MutationDefinition-class.Rd
man/HKL_S1F.Rd
man/expectedMutations.Rd
man/U5N.Rd
man/minNumMutationsTune.Rd
man/extendSubstitutionMatrix.Rd
man/calcObservedMutations.Rd
man/writeTargetingDistance.Rd
man/observedMutations.Rd
man/collapseClones.Rd
man/getPlatform.Rd
man/findThreshold.Rd
man/MK_RS1NF.Rd
man/createMutabilityMatrix.Rd
man/getBaselineStats.Rd
man/createSubstitutionMatrix.Rd
man/GmmThreshold-class.Rd
man/calcTargetingDistance.Rd
man/MK_RS5NF.Rd
man/makeAverage1merMut.Rd
man/createRegionDefinition.Rd
man/makeDegenerate5merMut.Rd
man/plotBaselineSummary.Rd
man/extendMutabilityMatrix.Rd
man/plotGmmThreshold.Rd
man/createTargetingModel.Rd
man/shmulateSeq.Rd
man/slideWindowSeq.Rd
man/minNumSeqMutationsTune.Rd
man/makeAverage1merSub.Rd
man/distToNearest.Rd
shazam documentation built on May 20, 2017, 4:48 a.m.

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