Decorates LFQData with methods to impute missing values

Decorates LFQData with methods to impute missing values

Decorates LFQData with methods to impute missing values

Details

Use `lfqdata$get_Imputer()` to create an instance. The imputer works on a deep copy of the data, so the original LFQData is not modified.

Typical workflow:

imp <- lfqdata$get_Imputer()
imp$impute(method = "multRepl", lod = "global")
imp$lfq$get_Plotter()$pca()

See also

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

Public fields

lfq

LFQData

Methods

Public methods

• LFQDataImp$new()

• LFQDataImp$impute()

• LFQDataImp$clone()

---

Method new()

initialize

Usage

LFQDataImp$new(lfqdata)

Arguments

lfqdata

LFQData object

---

Method impute()

Impute missing values using zCompositions

Usage

LFQDataImp$impute(
  method = c("multRepl", "GBM", "SQ", "BL", "CZM"),
  lod = c("global", "quantile")
)

Arguments

method

imputation method (default "multRepl")

lod

limit of detection strategy (default "global")

Returns

invisible(self) for chaining

---

Method clone()

The objects of this class are cloneable with this method.

Usage

LFQDataImp$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

dd <- prolfqua::sim_lfq_data_peptide_config()
#> creating sampleName from fileName column
#> completing cases
#> completing cases done
#> setup done
lfqdata <- LFQData$new(dd$data, dd$config)
imp <- LFQDataImp$new(lfqdata)
if (requireNamespace("zCompositions", quietly = TRUE)) {
  imp$impute(method = "multRepl", lod = "global")
  wide <- imp$lfq$to_wide(as.matrix = TRUE)
  stopifnot(!any(is.na(wide$data)))
}
#> Warning: Expected 2 pieces. Missing pieces filled with `NA` in 336 rows [1, 2, 3, 4, 5,
#> 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
#> Joining with `by = join_by(sampleName, protein_Id, peptide_Id)`