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shazam

February 20, 2016 Version 0.1.2

Somatic hypermutation analysis package.

Dependencies

R 3.1.2
R packages

  • alakazam
  • data.table
  • doParallel
  • dplyr
  • foreach
  • ggplot2
  • iterators
  • scales
  • SDMTools
  • seqinr
  • stringi
  • tidyr

Build Instructions

Install build dependencies:

install.packages(c("devtools", "roxygen2", "testthat", "knitr", "rmarkdown"))

Building with Rstudio:

  • Build -> Configure Build Tools
  • Check the Use devtools package functions option
  • Check the Generate documentation with Roxygen option
  • Select Configure... Roxygen options and check everything.
  • Build -> Build and Reload

Building from the R console:

devtools::install_deps()
devtools::document()
devtools::build()
devtools::install()

Optionally, you can skip the vignettes:

devtools::build(vignettes=FALSE)

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Version

Install

install.packages('shazam')

Monthly Downloads

1,122

Version

0.1.2

License

CC BY-NC-SA 4.0

Maintainer

Jason Vander Heiden

Last Published

February 21st, 2016

Functions in shazam (0.1.2)

createMutabilityMatrix

Builds a mutability model
shazam

The shazam package
getBaselineStats

Gets the summary statistics of a Baseline object
writeTargetingDistance

Write targeting model distances to a file
collapseByClone

Identifies clonal consensus sequences
calcBaseline

Calculate the BASELINe PDFs
clearConsole

Clears the console
calcExpectedMutations

Calculate expected mutation frequencies of a sequence
plotBaselineSummary

Plots BASELINe summary statistics
getnproc

Determines the numbers of CPU cores available
HS1FDistance

Human single nucleotide distance matrix.
createRegionDefinition

Creates a RegionDefinition
Baseline-class

S4 class defining a BASELINe (selection) object
IMGT_SCHEMES

IMGT unique numbering schemes
InfluenzaDb

Example Change-O database
calcTargetingDistance

Calculates a 5-mer distance matrix from a TargetingModel object
MutationDefinition-class

S4 class defining replacement and silent mutation definitions
extendSubstitutionMatrix

Extends a substitution model to include Ns.
createTargetingMatrix

Calculates a targeting rate matrix
U5NModel

Uniform 5-mer targeting model.
extendMutabilityMatrix

Extends a mutability model to include Ns.
createSubstitutionMatrix

Builds a substitution model
RegionDefinition-class

S4 class defining a region definition
getPlatform

Determines the OS platform being used
groupBaseline

Group BASELINe PDFs
M1NDistance

Mouse single nucleotide distance matrix.
calcObservedMutations

Count the number of observed mutations in a sequence.
calcDBObservedMutations

Calculate observed numbers of mutations
createMutationDefinition

Creates a MutationDefinition
distToNearest

Distance to nearest neighbor
plotBaselineDensity

Plots BASELINe probability density functions
HS5FModel

Human 5-mer targeting model.
MUTATION_SCHEMES

Amino acid mutation definitions
TargetingModel-class

S4 class defining a targeting model
createBaseline

Creates a Baseline object
plotMutability

Plot mutability probabilities
calcDBExpectedMutations

Calculate expected mutation frequencies
createTargetingModel

Creates a TargetingModel
summarizeBaseline

Calculate BASELINe summary statistics