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AggregateTopN

Source: R/LFQDataAggregator.R
AggregateTopN.Rd

AggregateTopN

AggregateTopN

Details

Aggregates peptide intensities to protein level using top N peptides. Works with raw (untransformed) intensities.

See also

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

Public fields

lfq

LFQData

lfq_agg

aggregation result

prefix

to use for aggregation results e.g. protein

N

top N peptides by intensity

func

aggregation function name: "sum" or "mean"

Methods

Public methods

Method new()

initialize

Usage

AggregateTopN$new(lfq, prefix = "protein", N = 3, func = "sum")

Arguments

lfq

LFQData

prefix

default protein

N

top N peptides (default 3)

func

"sum" or "mean" (default "sum")

Method aggregate()

run top N aggregation

Usage

AggregateTopN$aggregate()

Returns

LFQData

Method plot()

creates aggregation plots

Usage

AggregateTopN$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

AggregateTopN$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

AggregateTopN$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

istar <- prolfqua::sim_lfq_data_peptide_config()
#> creating sampleName from fileName column
#> completing cases
#> completing cases done
#> setup done
data <- istar$data |> dplyr::filter(protein_Id %in% sample(protein_Id, 100))
lfqdata <- LFQData$new(data, istar$config)

agg <- AggregateTopN$new(lfqdata, "protein", N = 3, func = "sum")
agg$aggregate()
#> Joining with `by = join_by(protein_Id, peptide_Id)`
#> Columns added : srm_meanInt srm_meanIntRank
p <- agg$plot()
p$plots[[1]]
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 4 rows containing missing values or values outside the scale range
#> (`geom_line()`).


agg_mean <- AggregateTopN$new(lfqdata, "protein", N = 3, func = "mean")
agg_mean$aggregate()
#> Joining with `by = join_by(protein_Id, peptide_Id)`
#> Columns added : srm_meanInt srm_meanIntRank
protPlotter <- agg_mean$lfq_agg$get_Plotter()
protPlotter$heatmap()

agg_mean$write_plots(tempdir())
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 4 rows containing missing values or values outside the scale range
#> (`geom_line()`).
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_line()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 5 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 3 rows containing missing values or values outside the scale range
#> (`geom_line()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_line()`).
#> Warning: Removed 8 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 6 rows containing missing values or values outside the scale range
#> (`geom_line()`).
#> Warning: Removed 3 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_line()`).
#> Warning: Removed 9 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 7 rows containing missing values or values outside the scale range
#> (`geom_line()`).