R/immunr_data_format.R
immunr_data_format.Rd
- "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.