ExampleMixedDb - 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