Impute missing values in a SummarizedExperiment object

Imputes missing values in a SummarizedExperiment object.

Usage

prot.impute(
  se,
  fun = c("bpca", "knn", "QRILC", "MLE", "MinDet", "MinProb", "man", "min", "zero",
    "mixed", "nbavg", "SampMin"),
  ...
)

Arguments

se

A SummarizedExperiment object

fun

A character string specifying the imputation method to use. The available methods are "bpca", "knn", "QRILC", "MLE", "MinDet", "MinProb", "man", "min", "zero", "mixed", "nbavg", and "SampMin".

...

Additional arguments passed to the imputation function.

Value

A SummarizedExperiment object with imputed values

Details

"SampMin" replaces missing values with the minimum value found in each sample. For information about the remaining imputation methods, see help("imputeMethods", "MsCoreUtils")

See also

prot.make_unique, prot.make_se

Examples

data(mset)
#> Warning: data set ‘mset’ not found
se <- make_se(mset)
#> Error: object 'mset' not found
se <- prot.impute(se, fun = "knn")
#> Error: object 'se' not found