AggregateLimpa

AggregateLimpa

AggregateLimpa

Details

Aggregates peptide/precursor intensities to protein level using limpa's probabilistic DPC-based quantification (limpa::dpcQuant). With impute_only = TRUE, performs same-level imputation without aggregation using limpa::dpcQuantByRow.

The output LFQData contains three value columns:

• intensity ("limpa") — protein-level log-expression (complete, no NAs)

• standard error (in config$opt_se) — per-protein, per-sample posterior SEs

• observation count (in config$nr_children) — number of observed precursors

See also

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

Public fields

lfq

LFQData (deep cloned input)

lfq_agg

aggregation result

prefix

to use for aggregation results e.g. protein

dpc_result

estimated DPC object from limpa::dpc

dpc_slope

DPC slope parameter (default 0.8)

impute_only

if TRUE use dpcQuantByRow (no aggregation)

Methods

Public methods

• AggregateLimpa$new()

• AggregateLimpa$aggregate()

• AggregateLimpa$plot()

• AggregateLimpa$write_plots()

• AggregateLimpa$clone()

---

Method new()

initialize

Usage

AggregateLimpa$new(
  lfq,
  prefix = "protein",
  dpc_slope = 0.8,
  impute_only = FALSE
)

Arguments

lfq

LFQData with log2-transformed intensities

prefix

default "protein"

dpc_slope

DPC slope parameter passed to limpa (default 0.8)

impute_only

if TRUE, use dpcQuantByRow instead of dpcQuant

---

Method aggregate()

run limpa DPC-based aggregation (or imputation)

Usage

AggregateLimpa$aggregate()

Returns

LFQData

---

Method plot()

creates aggregation plots (only for aggregation mode, not impute_only)

Usage

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

Arguments

subset

create plots for a subset of the data only

show.legend

default FALSE

Returns

data.frame

---

Method write_plots()

writes plots to folder

Usage

AggregateLimpa$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

---

Method clone()

The objects of this class are cloneable with this method.

Usage

AggregateLimpa$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

if (FALSE) { # \dontrun{
istar <- prolfqua::sim_lfq_data_peptide_config()
lfqdata <- LFQData$new(istar$data, istar$config)
lfqdata <- lfqdata$get_Transformer()$log2()$lfq

agg <- AggregateLimpa$new(lfqdata, "protein")
agg$aggregate()
agg$lfq_agg$to_wide()
} # }