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

In scoper: Spectral Clustering-Based Method for Identifying B Cell Clones

S4 class containing clonal assignments and summary data

Description

ScoperClones stores output from identicalClones, hierarchicalClones and spectralClones functions.

Usage

## S4 method for signature 'ScoperClones'
print(x)

## S4 method for signature 'ScoperClones'
summary(object)

## S4 method for signature 'ScoperClones,missing'
plot(x, y, ...)

## S4 method for signature 'ScoperClones'
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.

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

scoper documentation built on Oct. 6, 2023, 5:09 p.m.