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.
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 thereplace
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