ScoperClones-class - S4 class containing clonal assignments and summary data

Description¶

ScoperClones stores output from identicalClones, hierarchicalClones and spectralClones functions.

Usage¶

"print"(x)

"summary"(object)

"plot"(x, y, ...)

"as.data.frame"(x)

Arguments¶

x

ScoperClones object

object

ScoperClones object

y

ignored.

…

arguments to pass to plotCloneSummary.

Slots¶

db

data.frame of repertoire data including with clonal identifiers in the column specified during processing.

vjl_groups

data.frame of clonal summary, including sequence count, V gene, J gene, junction length, and clone counts. In single-cell mode, this summary is defined from heavy/long-chain partitions (IGH or TRB/TRD).

inter_intra

data.frame containing minimum inter (between) and maximum intra (within) clonal distances.

eff_threshold

effective cut-off separating the inter (between) and intra (within) clonal distances.

See also¶

identicalClones, hierarchicalClones and spectralClones