immunarch (version 0.10.3)

immunr_data_format: Specification of the data format used by immunarch dataframes

Description

• "Clones" - number of barcodes (events, UMIs) or reads;

• "Proportion" - proportion of barcodes (events, UMIs) or reads;

• "CDR3.nt" - CDR3 nucleotide sequence;

• "CDR3.aa" - CDR3 amino acid sequence;

• "V.name" - names of aligned Variable gene segments;

• "D.name" - names of aligned Diversity gene segments or NA;

• "J.name" - names of aligned Joining gene segments;

• "V.end" - last positions of aligned V gene segments (1-based);

• "D.start" - positions of D'5 end of aligned D gene segments (1-based);

• "D.end" - positions of D'3 end of aligned D gene segments (1-based);

• "J.start" - first positions of aligned J gene segments (1-based);

• "VJ.ins" - number of inserted nucleotides (N-nucleotides) at V-J junction (-1 for receptors with VDJ recombination);

• "VD.ins" - number of inserted nucleotides (N-nucleotides) at V-D junction (-1 for receptors with VJ recombination);

• "DJ.ins" - number of inserted nucleotides (N-nucleotides) at D-J junction (-1 for receptors with VJ recombination);

• "Sequence" - full nucleotide sequence.