RegionDefinition-class: S4 class defining a region definition
In shazam: Immunoglobulin Somatic Hypermutation Analysis

RegionDefinition-class

R Documentation

S4 class defining a region definition

Description

RegionDefinition defines a common data structure for defining the region boundaries of an Ig sequence.

Slots

name: name of the RegionDefinition.
description: description of the model and its source.
boundaries: factor defining the region boundaries of the sequence. The levels and values of boundaries determine the number of regions.
seqLength: length of the sequence.
regions: levels of the boundaries; e.g, c("cdr", "fwr").
labels: labels for the boundary and mutations combinations; e.g., c("cdr_r", "cdr_s", "fwr_r", "fwr_s").
citation: publication source.

See Also

See IMGT_SCHEMES for a set of predefined RegionDefinition objects.

shazam documentation built on Oct. 3, 2023, 1:06 a.m.

shazam index

Package overview README.md Distance to nearest neighbor Mutation analysis Selection quantification SHM targeting models Simulating sequence mutations Shazam: Inferring SHM targeting models Shazam: Mutation analysis Shazam: Quantification of selection pressure Shazam: Simulating sequence mutations Shazam: Tuning clonal assignment thresholds with nearest neighbor distances

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