impute_expt: Impute missing values using code from DEP reworked for...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Impute missing values using code from DEP reworked for expressionsets.

Description

[impute_expt()] imputes missing values in a proteomics dataset.

Usage

impute_expt(
  expt,
  filter = TRUE,
  p = 0.5,
  fun = c("bpca", "knn", "QRILC", "MLE", "MinDet", "MinProb", "min", "zero", "mixed",
    "nbavg"),
  ...
)

Arguments

expt	An ExpressionSet (well, expt), I think it is assumed that this should have been normalized and filtered for features which have no values across 'most' samples.
filter	Use normalize_expt() to filter the data?
p	When filtering with pofa, use this p parameter.
fun	"bpca", "knn", "QRILC", "MLE", "MinDet", "MinProb", "man", "min", "zero", "mixed" or "nbavg", Function used for data imputation based on [MSnbase::impute-methods()]
...	Additional arguments for imputation functions.

Value

An imputed expressionset.

See Also

[MSnbase]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.