ScoperClones-class function

S4 class containing clonal assignments and summary data

ScoperClones stores output from identicalClones , hierarchicalClones and spectralClones functions. class

## 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