shazam: Immunoglobulin Somatic Hypermutation Analysis

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.

Install the latest version of this package by entering the following in R:
install.packages("shazam")
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 publication2017-03-24 06:25:49 UTC
MaintainerJason Vander Heiden <jason.vanderheiden@yale.edu>
LicenseCC BY-SA 4.0
Version0.1.5
http://shazam.readthedocs.io

View on CRAN

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
calcBaseline Man page
calcExpectedMutations Man page
calcObservedMutations Man page
calcTargetingDistance Man page
CHARGE_MUTATIONS Man page
clearConsole Man page
collapseClones Man page
createBaseline Man page
createMutabilityMatrix Man page
createMutationDefinition Man page
createRegionDefinition Man page
createSubstitutionMatrix Man page
createTargetingMatrix Man page
createTargetingModel Man page
DensityThreshold Man page
DensityThreshold-class Man page
DensityThreshold-method Man page
distToNearest Man page
editBaseline Man page
expectedMutations Man page
extendMutabilityMatrix Man page
extendSubstitutionMatrix Man page
findThreshold Man page
getBaselineStats Man page
getnproc Man page
getPlatform Man page
GmmThreshold Man page
GmmThreshold-class Man page
GmmThreshold-method Man page
groupBaseline 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
makeAverage1merMut Man page
makeAverage1merSub Man page
makeDegenerate5merMut Man page
makeDegenerate5merSub Man page
minNumMutationsTune Man page
minNumSeqMutationsTune Man page
MK_RS1NF Man page
MK_RS5NF Man page
MutationDefinition Man page
MutationDefinition-class Man page
MUTATION_SCHEMES Man page
observedMutations Man page
plotBaselineDensity Man page
plotBaselineSummary Man page
plotDensityThreshold Man page
plot,DensityThreshold,missing-method Man page
plotGmmThreshold Man page
plot,GmmThreshold,missing-method Man page
plotMutability Man page
plotTune Man page
POLARITY_MUTATIONS Man page
print,DensityThreshold-method Man page
print,GmmThreshold-method Man page
RegionDefinition Man page
RegionDefinition-class Man page
shazam Man page
shazam-package Man page
shmulateSeq Man page
shmulateTree Man page
slideWindowDb Man page
slideWindowSeq Man page
slideWindowTune Man page
slideWindowTunePlot Man page
summarizeBaseline Man page
TargetingModel Man page
TargetingModel-class Man page
testBaseline Man page
U5N Man page
VOLUME_MUTATIONS Man page
writeTargetingDistance Man page

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/Targeting-Vignette.R
inst/doc/Targeting-Vignette.pdf
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/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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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