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alakazam (version 1.3.0)

AbundanceCurve-class: S4 class defining a clonal abundance curve

Description

AbundanceCurve defines clonal abundance values.

Usage

# S4 method for AbundanceCurve
print(x)
# S4 method for AbundanceCurve,missing
plot(x, y, ...)

Arguments

x

AbundanceCurve object

y

ignored.

...

arguments to pass to plotDiversityCurve.

Slots

abundance

data.frame with relative clonal abundance data and confidence intervals, containing the following columns:

  • group: group identifier.

  • clone_id or CLONE: clone identifier.

  • p: relative abundance of the clone.

  • lower: lower confidence inverval bound.

  • upper: upper confidence interval bound.

  • rank: the rank of the clone abundance.

bootstrap

data.frame of bootstrapped clonal distributions.

clone_by

string specifying the name of the clone column.

group_by

string specifying the name of the grouping column.

groups

vector specifying the names of unique groups in group column.

n

numeric vector indication the number of sequences sampled in each group.

nboot

numeric specifying the number of bootstrap iterations to use.

ci

confidence interval defining the upper and lower bounds (a value between 0 and 1).