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.

AuthorMohamed Uduman [aut], Gur Yaari [aut], Namita Gupta [aut], Jason Vander Heiden [aut, cre], Ang Cui [ctb], Susanna Marquez [ctb], Julian Zhou [ctb], Steven Kleinstein [aut, cph]
Date of publication2016-08-06 01:06:04
MaintainerJason Vander Heiden <jason.vanderheiden@yale.edu>
LicenseCC BY-NC-SA 4.0
Version0.1.4
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

distToNearest: Distance to nearest neighbor

expectedMutations: Calculate expected mutation frequencies

extendMutabilityMatrix: Extends a mutability model to include Ns.

extendSubstitutionMatrix: Extends a substitution model to include Ns.

getBaselineStats: Gets the summary statistics of a Baseline object

getnproc: Determines the numbers of CPU cores available

getPlatform: Determines the OS platform being used

groupBaseline: Group BASELINe PDFs

HS1FDistance: Human single nucleotide distance matrix.

HS5FModel: Human 5-mer targeting model.

IMGT_SCHEMES: IMGT unique numbering schemes

M1NDistance: Mouse single nucleotide distance matrix.

MRS5NFModel: Mouse 5-mer targeting model.

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

plotMutability: Plot mutability probabilities

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

summarizeBaseline: Calculate BASELINe summary statistics

TargetingModel-class: S4 class defining a targeting model

testBaseline: Two-sided test of BASELINe PDFs

U5NModel: Uniform 5-mer 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
distToNearest Man page
expectedMutations Man page
extendMutabilityMatrix Man page
extendSubstitutionMatrix Man page
getBaselineStats Man page
getnproc Man page
getPlatform Man page
groupBaseline Man page
HS1FDistance Man page
HS5FModel Man page
HYDROPATHY_MUTATIONS Man page
IMGT_SCHEMES Man page
IMGT_V Man page
IMGT_V_BY_REGIONS Man page
IMGT_V_BY_REGIONS_NO_CDR3 Man page
IMGT_V_NO_CDR3 Man page
M1NDistance Man page
MRS5NFModel Man page
MutationDefinition Man page
MutationDefinition-class Man page
MUTATION_SCHEMES Man page
observedMutations Man page
plotBaselineDensity Man page
plotBaselineSummary Man page
plotMutability Man page
POLARITY_MUTATIONS Man page
RegionDefinition Man page
RegionDefinition-class Man page
shazam Man page
shazam-package Man page
shmulateSeq Man page
shmulateTree Man page
summarizeBaseline Man page
TargetingModel Man page
TargetingModel-class Man page
testBaseline Man page
U5NModel Man page
VOLUME_MUTATIONS Man page
writeTargetingDistance Man page

Files

shazam
shazam/inst
shazam/inst/CITATION
shazam/inst/doc
shazam/inst/doc/Baseline-Vignette.R
shazam/inst/doc/DistToNearest-Vignette.pdf
shazam/inst/doc/Baseline-Vignette.pdf
shazam/inst/doc/DistToNearest-Vignette.Rmd
shazam/inst/doc/Targeting-Vignette.Rmd
shazam/inst/doc/DistToNearest-Vignette.R
shazam/inst/doc/Targeting-Vignette.R
shazam/inst/doc/Targeting-Vignette.pdf
shazam/inst/doc/Baseline-Vignette.Rmd
shazam/inst/markr
shazam/inst/markr/build.R
shazam/NAMESPACE
shazam/NEWS.md
shazam/data
shazam/data/VOLUME_MUTATIONS.rda
shazam/data/HYDROPATHY_MUTATIONS.rda
shazam/data/CHARGE_MUTATIONS.rda
shazam/data/POLARITY_MUTATIONS.rda
shazam/data/M1NDistance.rda
shazam/data/IMGT_V_BY_REGIONS.rda
shazam/data/MRS5NFModel.rda
shazam/data/IMGT_V_NO_CDR3.rda
shazam/data/IMGT_V.rda
shazam/data/HS5FModel.rda
shazam/data/U5NModel.rda
shazam/data/IMGT_V_BY_REGIONS_NO_CDR3.rda
shazam/data/HS1FDistance.rda
shazam/R
shazam/R/DistToNearest.R shazam/R/Core.R shazam/R/Shmulate.R
shazam/R/sysdata.rda
shazam/R/Baseline.R shazam/R/Shazam.R shazam/R/TargetingModels.R shazam/R/RegionDefinitions.R shazam/R/MutationDefinitions.R shazam/R/MutationProfiling.R
shazam/vignettes
shazam/vignettes/DistToNearest-Vignette.Rmd
shazam/vignettes/Targeting-Vignette.Rmd
shazam/vignettes/Baseline-Vignette.Rmd
shazam/README.md
shazam/MD5
shazam/build
shazam/build/vignette.rds
shazam/DESCRIPTION
shazam/man
shazam/man/MRS5NFModel.Rd shazam/man/clearConsole.Rd shazam/man/Baseline-class.Rd shazam/man/shmulateTree.Rd shazam/man/TargetingModel-class.Rd shazam/man/createMutationDefinition.Rd shazam/man/calcExpectedMutations.Rd shazam/man/plotMutability.Rd shazam/man/HS5FModel.Rd shazam/man/shazam.Rd shazam/man/RegionDefinition-class.Rd shazam/man/summarizeBaseline.Rd shazam/man/calcBaseline.Rd shazam/man/plotBaselineDensity.Rd shazam/man/createBaseline.Rd shazam/man/IMGT_SCHEMES.Rd shazam/man/getnproc.Rd shazam/man/testBaseline.Rd shazam/man/createTargetingMatrix.Rd shazam/man/MUTATION_SCHEMES.Rd shazam/man/groupBaseline.Rd shazam/man/MutationDefinition-class.Rd shazam/man/expectedMutations.Rd shazam/man/U5NModel.Rd shazam/man/extendSubstitutionMatrix.Rd shazam/man/calcObservedMutations.Rd shazam/man/writeTargetingDistance.Rd shazam/man/observedMutations.Rd shazam/man/collapseClones.Rd shazam/man/getPlatform.Rd shazam/man/createMutabilityMatrix.Rd shazam/man/getBaselineStats.Rd shazam/man/createSubstitutionMatrix.Rd shazam/man/calcTargetingDistance.Rd shazam/man/createRegionDefinition.Rd shazam/man/plotBaselineSummary.Rd shazam/man/extendMutabilityMatrix.Rd shazam/man/HS1FDistance.Rd shazam/man/createTargetingModel.Rd shazam/man/shmulateSeq.Rd shazam/man/M1NDistance.Rd shazam/man/distToNearest.Rd

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

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

All documentation is copyright its authors; we didn't write any of that.