Method to impute SummarizedExperiment. This method performs a mixed imputation on the proteins. It uses a k-nearest neighbor imputation for proteins with missing values at random (MAR) and imputes missing values by random draws from a left-shifted Gaussian distribution for proteins with missing values not at random (MNAR).

Method to impute SummarizedExperiment. This method performs a mixed imputation on the proteins. It uses a k-nearest neighbor imputation for proteins with missing values at random (MAR) and imputes missing values by random draws from a left-shifted Gaussian distribution for proteins with missing values not at random (MNAR).

Usage

impute_se(se, ain = NULL, condition = NULL)

Arguments

se

SummarizedExperiment containing all necessary information of the proteomics dataset

ain

Vector of strings which assay should be used as input (default NULL). If NULL then all normalization of the se object are plotted next to each other.

condition

name of column of colData(se) representing the conditions of the data

Value

SummarizedExperiment with imputed intensities

Examples

data(tuberculosis_TMT_se)
tuberculosis_TMT_se <- remove_samples_manually(tuberculosis_TMT_se,
                          column = "Label", values = c("1.HC_Pool1"))
#> 1 samples removed.
tuberculosis_TMT_se <- impute_se(tuberculosis_TMT_se, ain = NULL,
                          condition = NULL)
#> Condition of SummarizedExperiment used!
#> All assays of the SummarizedExperiment will be used.
#> Imputing along margin 1 (features/rows).
#> Imputing along margin 1 (features/rows).
#> Imputing along margin 1 (features/rows).
#> Imputing along margin 1 (features/rows).
#> Imputing along margin 1 (features/rows).
#> Imputing along margin 1 (features/rows).