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dowser (version 2.2.0)

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

Arguments

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