ChangeoClone-class: S4 class defining a clone

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

S4 class defining a clone

Description

ChangeoClone defines a common data structure for perform lineage recontruction from Change-O data.

Slots

data

data.frame containing sequences and annotations. Contains the columns SEQUENCE_ID and SEQUENCE, as well as any additional sequence-specific annotation columns.

clone

string defining the clone identifier.

germline

string containing the germline sequence for the clone.

v_gene

string defining the V segment gene call.

j_gene

string defining the J segment gene call.

junc_len

numeric junction length (nucleotide count).

See Also

See makeChangeoClone and buildPhylipLineage for use.

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.