Base class of the peptide to protein aggregators

Holds the fields, construction, and plotting shared by AggregateMedpolish, AggregateRlm, AggregateTopN and AggregateLimpa. Subclasses implement aggregate().

Value

An R6 class generator.

See also

Other LFQData: AggregateLimpa, AggregateMedpolish, AggregateRlm, AggregateTopN, LFQData, LFQDataPlotter, LFQDataStats, LFQDataSummariser, LFQDataToSummarizedExperiment()

Public fields

lfq

LFQData

lfq_agg

aggregation result

prefix

to use for aggregation results e.g. protein

Methods

Public methods

• AggregatorBase$new()

• AggregatorBase$plot()

• AggregatorBase$write_plots()

• AggregatorBase$clone()

---

AggregatorBase$new()

initialize

Usage

AggregatorBase$new(lfq, prefix = "protein")

Arguments

lfq

LFQData

prefix

default protein

---

AggregatorBase$plot()

creates aggregation plots

Usage

AggregatorBase$plot(subset = NULL, show.legend = FALSE)

Arguments

subset

create plots for a subset of the data only

show.legend

default FALSE

Returns

data.frame

---

AggregatorBase$write_plots()

writes plots to folder

Usage

AggregatorBase$write_plots(
  qcpath,
  subset = NULL,
  show.legend = FALSE,
  width = 6,
  height = 6
)

Arguments

qcpath

qcpath

subset

write plots only for some

show.legend

legend

width

figure width

height

figure height

Returns

file path

---

AggregatorBase$clone()

The objects of this class are cloneable with this method.

Usage

AggregatorBase$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.