ExampleMixedDb {dowser}

Example Change-O database

Description

A small example database subset from Turner, J. S. et al. Human germinal centres engage memory and naive B cells after influenza vaccination. Nature 586, 127–132 (2020).

Usage

ExampleMixedDb

Format

A data.frame with the following Change-O style columns:

• sequence_id: Sequence identifier

• sequence: B cell sequence

• productive: A logical indicating if the sequence is productive.

• v_call: V region allele assignments.

• d_call: D region allele assignments.

• j_call: J region allele assignments.

• sequence_alignment: Sequence alignment.

• germline_alignment: Germline alignment without gaps.

• junction: Junction

• juncation_aa: Junction aa

• vj_inframe: A logical to see if the vj genes are in frame

• stop_codon: A indicator if there is a stop codon within the alignment

• locus: Locus identifier.

• v_sequence_start: Where the V gene starts

• v_sequence_end: Where the V gene ends

• v_germline_start: Where the V germline starts

• v_germline_end: Where the V germline ends

• np1_length: Length of np1

• d_sequence_start: Where the D gene starts

• d_sequence_end: Where the D gene ends

• d_germline_start: Where the D germline starts

• d_germline_end: Where the D germline ends

• np2_length: Length of np2

• j_sequence_start: Where the J gene starts

• j_sequence_end: Where the J gene ends

• j_germline_start: Where the J germline starts

• j_germline_end: Where the J germline ends

• junction_length: Length of the junction region in nucleotides.

• v_score: V score

• v_identity: Identity score of V

• v_support: V support

• d_score: D score

• d_identity: D identity

• d_support: D support

• j_score: J score

• j_support: J support

• j_identity: J identity

• cell_id: Cell identifier

• consensus_count: Consensus count

• indels: Logical if indels are present

• sequence_vdj: VDJ sequence

• v_germ_start_vdj: Where the V germline starts on the VDJ

• v_germ_end_vdj: Where the V germline ends on the VDJ

• subject: Subject identifier

• timepoint: Day the sample was taken

• cell_type: Type of cell

• replicate: Replicate number

• clone_id: Change-O assignment clonal group identifier.

• seq_type: Identifier of data type (10x)

• vj_gene: VJ gene

• vj_alt_gene: Alternative VJ gene

• v_germline_length: Length of the V germline segment

• d_germline_length: Length of the D germline segment

• j_germline_lenght: Length of the J germline segment

• germline_alignment_d_mask: Germline alignment with gaps