analyzeClones - Clonal assignment analysis
analyzeClones function performs a series of analysis to assess the performance of
analyzeClones(db, junction = "JUNCTION", v_call = "V_CALL", j_call = "J_CALL", clone = "CLONE", first = FALSE, cdr3 = FALSE, nproc = 1, progress = FALSE)
- 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.
- name of the data column containing clone identifiers.
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).
- number of cores to distribute the function over.
TRUEprint a progress bar.
Returns a ClonalAnalysis object.
cdr3 must match the corresponding arguments
used in the defineClonesScoper function.
# Clonal assignment analysis results <- analyzeClones(ClonedExampleDb, junction = "JUNCTION", v_call = "V_CALL", j_call = "J_CALL", clone = "CLONE", first = TRUE) # print threshold (a numeric) results@threshold
# get inter and intra conal distances (a data.frame) df <- results@inter_intra[] # density plot of inter versus intra clonal distances (a ggplot). results@plot_inter_intra
# get the neighborhoods used in spectral clustering (a numeric vector). ngs <- results@neighborhoods # plot histogram of neighborhoods (a ggplot). results@plot_neighborhoods