LFQDataAggregator: Decorates LFQData with methods to aggregate protein...

In wolski/prolfqua: Proteomics Label Free Quantification

Decorates LFQData with methods to aggregate protein intensities aggregates intensities

Description

Decorates LFQData with methods to aggregate protein intensities aggregates intensities

Decorates LFQData with methods to aggregate protein intensities aggregates intensities

Public fields

lfq

LFQData

lfq_agg

aggregation result

prefix

to use for aggregation results e.g. protein

Methods

Public methods

• LFQDataAggregator$new()

• LFQDataAggregator$medpolish()

• LFQDataAggregator$lmrob()

• LFQDataAggregator$mean_topN()

• LFQDataAggregator$sum_topN()

• LFQDataAggregator$plot()

• LFQDataAggregator$write_plots()

• LFQDataAggregator$clone()

---

Method new()

initialize

Usage

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

Arguments

lfq

LFQData

prefix

default protein

---

Method medpolish()

aggregate using median polish

Usage

LFQDataAggregator$medpolish()

Arguments

N

top N by intensity

Returns

LFQData

---

Method lmrob()

aggregate using robust regression

Usage

LFQDataAggregator$lmrob()

Arguments

N

top N by intensity

Returns

LFQData

---

Method mean_topN()

aggregate topN using mean

Usage

LFQDataAggregator$mean_topN(N = 3)

Arguments

N

top N by intensity

Returns

LFQData

---

Method sum_topN()

aggregate topN using sum

Usage

LFQDataAggregator$sum_topN(N = 3)

Arguments

N

top N by intensity

Returns

LFQData

---

Method plot()

creates aggregation plots

Usage

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

Arguments

subset

create plots for a subset of the data only, e.g. proteins with more then 2 peptides.

show.legend

default FALSE

Returns

data.frame

---

Method write_plots()

writes plots to folder

Usage

LFQDataAggregator$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

LFQDataAggregator$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

See Also

Other LFQData: LFQData, LFQDataPlotter, LFQDataStats, LFQDataSummariser, LFQDataToSummarizedExperiment(), LFQDataWriter

Examples

istar <-  prolfqua::sim_lfq_data_peptide_config()
istar$config <- istar$config
data <- istar$data |> dplyr::filter(protein_Id %in% sample(protein_Id, 100))
lfqdata <- LFQData$new(data, istar$config)

lfqTrans <- lfqdata$clone()$get_Transformer()
lfqTrans$log2()
lfqTrans <- lfqTrans$robscale()$lfq
lfqAggregator <- LFQDataAggregator$new(lfqTrans, "protein")

lfqAggregator$medpolish()
pmed <- lfqAggregator$plot()
pmed$plots[[1]]
lfqAggregator$lmrob()
prob <- lfqAggregator$plot()
prob$plots[[1]]

lfqCopy <- lfqdata$clone()
lfqCopy$is_transformed()
lfqAggregator <- LFQDataAggregator$new(lfqCopy, "protein")
lfqAggregator$sum_topN()
pSum <- lfqAggregator$plot()
pSum$plots[[1]]

lfqAggregator$mean_topN()
pMean <- lfqAggregator$plot()
pMean$plots[[1]]
protPlotter <- lfqAggregator$lfq_agg$get_Plotter()
protPlotter$heatmap()
## Not run: 
lfqAggregator$write_plots(tempdir())

## End(Not run)

wolski/prolfqua documentation built on Sept. 7, 2024, 3:06 a.m.