shazam1.2.0 package

S4 class defining a BASELINe (selection) object

Calculate the BASELINe PDFs (including for regions that include CDR3 a...

Calculate expected mutation frequencies of a sequence

Count the number of observed mutations in a sequence.

Calculates a 5-mer distance matrix from a TargetingModel object

Calculate total mutability

Constructs effective clonal sequences for all clones

Construct a consensus sequence

convertNumbering: IMGT-Kabat number conversion

Creates a Baseline object

Builds a mutability model

Creates a MutationDefinition

Creates a RegionDefinition

Builds a substitution model

Calculates a targeting rate matrix

Creates a TargetingModel

Output of the dens method of findThreshold

Distance to nearest neighbor

Edit the Baseline object

Calculate expected mutation frequencies

Extends a mutability model to include Ns.

Extends a substitution model to include Ns.

Find distance threshold

Output of the gmm method of findThreshold

Group BASELINe PDFs

IMGT unique numbering schemes

Make a 1-mer mutability model by averaging over a 5-mer mutability mod...

Make a 1-mer substitution model by averaging over a 5-mer substitution...

Make a degenerate 5-mer mutability model based on a 1-mer mutability m...

Make a degenerate 5-mer substitution model based on a 1-mer substituti...

Build a data.frame from a ChangeoClone and an igraph object containing...

Parameter tuning for minNumMutations

Parameter tuning for minNumSeqMutations

S4 class defining a mutability model

Amino acid mutation definitions

S4 class defining replacement and silent mutation definitions

Calculate observed numbers of mutations

Plots BASELINe probability density functions

Plots BASELINe summary statistics

Plot findThreshold results for the density method

Plot findThreshold results for the gmm method

Plot mutability probabilities

Visualize parameter tuning for sliding window approach

Visualize parameter tuning for minNumMutations and minNumSeqMutations

S4 class defining a region definition

Build a RegionDefinition object that includes CDR3 and FWR4.

shazam: Immunoglobulin Somatic Hypermutation Analysis

The shazam package

Simulate mutations in a single sequence

Simulate mutations in a lineage tree

Sliding window approach towards filtering sequences in a data.frame

Sliding window approach towards filtering a single sequence

Parameter tuning for sliding window approach

slideWindowTunePlot - plotSlideWindowTune backward compatability

Calculate BASELINe summary statistics

S4 class defining a targeting matrix

S4 class defining a targeting model

Two-sided test of BASELINe PDFs

Write targeting model distances to a file