scoper (version 0.1.0)

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.

Examples

# NOT RUN {
# 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[[1]]

# 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
# }