clones.shared: Shared clones between samples
In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

Description Usage Arguments Details Value Note Author(s) See Also Examples

clones.shared compares clones of different samples to find shared clones with identical or similar CDR3 sequences. Criteria for same/similar clones are 1) same CDR3 length, 2) CDR3 identity of a given treshold, 3) same V gene, 4) same J gene (optional). Parallel processing is possible.

clones.shared.summary provides information about the number of shared clones between two or more samples.

clones.shared(clones.tab = NULL, identity = 0.85, useJ = TRUE, dispD = TRUE, 
     dispCDR3aa = FALSE, dispCDR3nt = FALSE, dispFunctionality.list = FALSE, 
     dispFunctionality.ratio = FALSE, dispJunctionFr.list = FALSE, 
     dispJunctionFr.ratio = FALSE, dispTotalSeq = FALSE, nrCores=1)

clones.shared.summary(shared.tab = NULL, clones.tab = NULL)

`clones.tab`	A dataframe, which includes all individual clones. Therefore data frames, as output from `clones()` has to be combined, via `rbind()`. The first column needs to include individual identifiers. Example: `data(ClonesAllInd)`
`identity`	A Value between 0 and 1, indicating proportion of identity of sequences.
`useJ`	TRUE: J gene shall be included as criteria (default: TRUE)
`dispD`	TRUE: return D gene and allele in output data frame (only, if they are included in input; default: TRUE)
`dispCDR3aa`	TRUE: return CDR3 amino acid sequences in output data frame (only, if they are included in input; default: FALSE)
`dispCDR3nt`	TRUE: return CDR3 nucleotide sequences in output data frame (only, if they are included in input; default: FALSE)
`dispFunctionality.list`	TRUE: return functionality list in output data frame (only, if they are included in input; default: FALSE)
`dispFunctionality.ratio`	TRUE: return functionality ratios for prosuctive and unproductive sequences in output data frame (only, if they are included in input; default: FALSE)
`dispJunctionFr.list`	TRUE: return junction frame list in output data frame (only, if they are included in input; default: FALSE)
`dispJunctionFr.ratio`	TRUE: return junction frame ratios for in-frame and out-of-frame sequences output data frame (only, if they are included in input; default: FALSE)
`dispTotalSeq`	TRUE: return total nucleotide sequences output data frame (only, if they are included in input; default: FALSE)
`nrCores`	Number of cores used for parallel processing (default: 1)
`shared.tab`	Output from function `clones.shared()`. Either whole data frame or individual column.

clones.shared: Criteria for clone groups are 1) same CDR3 length, 2) CDR3 identity of a given treshold, 3) same V gene and 4) same J gene (optional). Same or similar CDR3 sequences has to be shared between at least two samples. A treshold for CDR3 identity has to be between 0 and 1. A cutoff of 0.85 means CDR3 identity of 85%. For example for a CDR3 length of 15 amino acids 85% identity would mean that at least 11 of 15 positions have to be identical (0.85*15 = 10.75; values are rounded).

useJ=T includes also the criteria of same J genes for clone defintion.

clones.shared.summary summarizes information about shared clones. If clonestab.individual is also provided, number of clones, appearing in only one of these individuals is also returned.

Output of clones.shared is a data frame including

`number_samples`	The number of samples, that share this clones
`samples`	Sample ID's, seperated by ";"
`CDR3_length_AA`	length of CDR3 amino acid sequence
`shared_CDR3`	shared (100% identity) or similar (<100% identity) CDR3 sequence
`number_shared_CDR3`	Number of shared CDR3 sequences
`unique_CDR3_sequences_AA_per_individual`	CDR3 sequences per clone, individuals are seperated by ";"
`sequence_count_per_CDR3`	Quantity how often clones of "unique all CDR3 sequences [AA] per individual" appaer, individuals are seperated by ";"
`V_gene`	V gene
`J_gene`	J gene(s)
`optional output`	D_gene; all_CDR3_sequences_AA; al_CDR3_sequences_nt; Funct_all_sequences; Funct_productive/unproductive; Junction_frame_all_sequences; JF_in-frame/out-of-frame; Total_sequences_nt (individuals are seperated by ";")

Output of clones.shared.summary is a data frame containing all possible groups and the quantity of appearance.

For large datasets computational time can be extensive.

Julia Bischof

clones

## Not run: 
data(clones.allind)
sharedclones<-clones.shared(clones.tab = clones.allind, identity = 0.85, useJ = TRUE, 
     dispD = TRUE, dispCDR3aa = TRUE)
sharedclones.summary<-clones.shared.summary(shared.tab = sharedclones)

## End(Not run)