clones.shared: Shared clones between individuals

Description

clones.shared compares clones of different individuals 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). clones.shared.summary provides information about the number of shared clones between two or more individuals.

Usage

clones.shared(clones.tab = NULL, identity = 0.85, useJ = TRUE, dispD = TRUE, 
     dispCDR3aa = TRUE, 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)

Arguments

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: TRUE)

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.

Value

Output of clones.shared is a data frame including
number_individualsThe number of individuals, that share this clones
individualsIndividual ID's, seperated by ";"
CDR3_length_AAlength of CDR3 amino acid sequence
shared_CDR3shared (100% identity) or similar (<100% identity)="" cdr3="" sequence<="" description="">
number_shared_CDR3Number of shared CDR3 sequences
unique_CDR3_sequences_AA_per_individualCDR3 sequences per clone, individuals are seperated by ";"
sequence_count_per_CDR3Quantity how often clones of "unique all CDR3 sequences [AA] per individual" appaer, individuals are seperated by ";"
V_geneV gene
J_geneJ gene(s)
optional outputD_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.

Details

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 sequence has to be shared between at least two individuals. 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 up). 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.

Examples

Run this code

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)