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normByFullProteome normalizes the phosphoproteome data by the corresponding full proteome data in a MultiAssayExperiment object. The "Phosphoproteome" assay in the MultiAssayExperiment will be replaced by the ratio.

Usage

normByFullProteome(mae, replace = TRUE)

Arguments

mae

A MultiAssayExperiment object containing both phosphoproteome and proteome assays.

replace

Logical, whether to replace the existing phosphoproteome assay in the MultiAssayExperiment object. If replace = FALSE, a new assay, phosphoRatio, will be created. Default is TRUE.

Value

A MultiAssayExperiment object with the normalized phosphoproteome data.

Details

The function performs the following steps:

  • Checks if both phosphoproteome and proteome assays are present in the MultiAssayExperiment object.

  • Extracts the phosphoproteome and proteome assays along with the sample annotations.

  • Matches the samples between the phosphoproteome and proteome assays.

  • Normalizes the phosphoproteome data by dividing it by the corresponding proteome data.

  • Replaces the phosphoproteome assay in the MultiAssayExperiment object or adds the normalized data as a new assay, depending on the replace parameter.

Examples

# load mae object
data("dia_example")
# call the function
normByFullProteome(dia_example)
#> harmonizing input:
#>   removing 27 sampleMap rows with 'colname' not in colnames of experiments
#> A MultiAssayExperiment object of 2 listed
#>  experiments with user-defined names and respective classes.
#>  Containing an ExperimentList class object of length 2:
#>  [1] Phosphoproteome: SummarizedExperiment with 4 rows and 20 columns
#>  [2] Proteome: SummarizedExperiment with 500 rows and 47 columns
#> Functionality:
#>  experiments() - obtain the ExperimentList instance
#>  colData() - the primary/phenotype DataFrame
#>  sampleMap() - the sample coordination DataFrame
#>  `$`, `[`, `[[` - extract colData columns, subset, or experiment
#>  *Format() - convert into a long or wide DataFrame
#>  assays() - convert ExperimentList to a SimpleList of matrices
#>  exportClass() - save data to flat files