analyzeClones - Clonal assignment analysis

Description

The analyzeClones function performs a series of analysis to assess the performance of defineClonesScoper function.

Usage

analyzeClones(db, junction = "JUNCTION", v_call = "V_CALL",
j_call = "J_CALL", clone = "CLONE", first = FALSE, cdr3 = FALSE,
nproc = 1, progress = FALSE)

Arguments

db
data.frame with Change-O style columns containing sequence data.
junction
name of the column containing nucleotide sequences to compare. Also used to determine sequence length for grouping.
v_call
name of the column containing the V-segment allele calls.
j_call
name of the column containing the J-segment allele calls.
clone
name of the data column containing clone identifiers.
first
if TRUE only the first call of the gene assignments is used. if FALSE the union of ambiguous gene assignments is used to group all sequences with any overlapping gene calls.
cdr3
if TRUE remove 3 nts from both ends of junction (converts IMGT junction to CDR3 region).
nproc
number of cores to distribute the function over.
progress
if TRUE print a progress bar.

Value

Returns a ClonalAnalysis object.

Note

Arguments first and cdr3 must match the corresponding arguments used in the defineClonesScoper function.

Examples

# 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

[1] 0.23


# get inter and intra conal distances (a data.frame)
df <- results@inter_intra[[1]]

# density plot of inter versus intra clonal distances  (a ggplot).
results@plot_inter_intra

[[1]]

5




# get the neighborhoods used in spectral clustering (a numeric vector).
ngs <- results@neighborhoods

# plot histogram of neighborhoods (a ggplot).
results@plot_neighborhoods
[[1]]

9