Description Usage Arguments Details Value Note Author(s) See Also Examples
This function uses IMGT/HighV-QUEST output files to define B cell clones. Therefore criteria using amino acid CDR3 sequences, V genes and J genes (optional) are used. A treshold for CDR3 identity/similarity can be given. Parallel processing is possible.
1 2 3 4 5 | clones(aaseqtab = NULL, summarytab = NULL, ntseqtab = NULL, identity = 0.85,
useJ = TRUE,dispD = FALSE, dispSeqID = FALSE, dispCDR3aa = FALSE,
dispCDR3nt = FALSE, dispJunctionFr.ratio = FALSE,
dispJunctionFr.list = FALSE, dispFunctionality.ratio = FALSE,
dispFunctionality.list = FALSE, dispTotalSeq = FALSE, nrCores=1)
|
aaseqtab |
IMGT/HighV-QUEST output, file 5_AA-sequences(...).txt |
summarytab |
IMGT/HighV-QUEST output, file 1_Summary(...).txt |
ntseqtab |
IMGT/HighV-QUEST output, file 3_Nt-sequences(...).txt (optional) |
identity |
Treshold of CDR3 identity. A value between 0 and 1. |
useJ |
Shall J genes be included into analysis? default: TRUE |
dispD |
Shall D genes and alleles be returned? default: FALSE |
dispSeqID |
Shall sequence ID's be returned? default: FALSE |
dispCDR3aa |
Shall amino acid CDR3 sequences be returned? default: FALSE |
dispCDR3nt |
Shall nucleotide amino acid sequences be returned? default: FALSE |
dispJunctionFr.ratio |
Shall ratios of in-frame, out-of-frame and unknown junctions be returned? default: FALSE |
dispJunctionFr.list |
Shall a list of all junction frames be returned? default: FALSE |
dispFunctionality.ratio |
Shall ratios of productive, unproductive and unknown functionality sequences be returned? default: FALSE |
dispFunctionality.list |
Shall a list of all functionalities be returned? default: FALSE |
dispTotalSeq |
Shall all total nucleotide sequences be returned? default: FALSE |
nrCores |
Number of cores used for parallel processing (default: 1) |
This function uses IMGT/HighV-QUEST output to define clones. Therefore amino acid CDR3 sequences, V genes and J genes (optional) are used. 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). 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.
Important to know:
- if useJ=T
, sequences having no J information are ignored
Output of clones() is a data frame containing
unique_CDR3_sequences_[AA] |
unique CDR3 sequences belonging to this clone |
CDR3_length_AA |
CDR3 length in amino acids |
number_of_unique_sequences |
number of unique CDR3 sequences belonging to this clone |
total_number_of_sequences |
number of all sequences belonging to this clone (one sequence can appear several times) |
sequence_count_per_CDR3 |
sequence count for each of the unique CDR3 sequences |
V_gene |
V gene belonging to this clone |
V_gene_and_allele |
original IMGT V gene nomenclature |
J_gene |
J gene(s) belonging to this clone (if useJ=F, there can be several J genes) |
J_gene_and_allele |
original IMGT J gene nomenclature |
optional arguments |
D_gene;_all_CDR3_sequences_AA; all_CDR3_sequences_nt; Funct_all_sequences; Funct_productive/unproductive/unknown sequences; Junction_frame_all_sequences; JF_in-frame/out-of-frame/unknown sequences; Sequence_IDs; Total_sequences_nt |
For large datasets computational time can be extensive.
Julia Bischof
clones.CDR3Length
, plotClonesCDR3Length
, plotClonesCopyNumber
, geneUsage
,
1 2 3 4 5 6 7 8 | ## Not run:
data(summarytab)
data(aaseqtab)
clones.tab<-clones(aaseqtab=aaseqtab,summarytab=summarytab, identity=0.85, useJ=TRUE,
dispCDR3aa=TRUE, dispFunctionality.ratio=TRUE, dispFunctionality.list=TRUE)
## End(Not run)
|
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