defineClonesScoper - Assigning Ig sequences into clonal groups
defineClonesScoper function provides an unsupervised pipline for assigning Ig sequences into
clonal groups sharing same V gene, J gene, and junction length.
defineClonesScoper(db, junction = "JUNCTION", v_call = "V_CALL", j_call = "J_CALL", first = FALSE, cdr3 = FALSE, mod3 = FALSE, iter_max = 1000, nstart = 25, nproc = 1, progress = FALSE, out_name = NULL, out_dir = ".")
- data.frame with Change-O style columns containing sequence data.
- name of the column containing nucleotide sequences to compare. Also used to determine sequence length for grouping.
- name of the column containing the V-segment allele calls.
- name of the column containing the J-segment allele calls.
TRUEonly the first call of the gene assignments is used. if
FALSEthe union of ambiguous gene assignments is used to group all sequences with any overlapping gene calls.
TRUEremove 3 nts from both ends of
junction(converts IMGT junction to CDR3 region). if
junction(s) with length less than 7 nts.
junction(s) with number of nucleotides not modulus of 3.
- the maximum number of iterations allowed for kmean clustering step.
- the number of random sets chosen for kmean clustering initialization.
- number of cores to distribute the function over.
TRUEprint a progress bar.
- if not
NULLsave cloned data.frame and a summary of cloning performance.
out_namestring is used as the prefix of the successfully processed output files.
- specify to change the output directory. The input file
directory is used if this is not specified while
Returns a modified
db data.frame with clone identifiers in the
out_name is not
NULL, it will save the modified
db and a summary
of cloning performance in the current directory or the specified
An unsupervised pipeline to identify B cell clones from adaptive immune receptor repertoire sequencing (AIRR-Seq) datasets. This method is based on spectral clustering of the junction sequences of B cell receptors (BCRs, also referred to as Immunoglobulins, (Igs)) that share the same V gene, J gene and junction length. It uses an adaptive threshold that analyzes sequences in a local neighborhood.
# clone data using defineClonesScoper function db <- defineClonesScoper(ExampleDb, junction = "JUNCTION", v_call = "V_CALL", j_call = "J_CALL", first = TRUE)
CLONES= 1058 RECORDS= 2000 PASS= 2000 FAIL= 0
To assess the performance of clonal assignment process check