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Preprocess Proteome Data

Source: R/preprocess_proteome_phospho.R
preprocessProteome.Rd

preprocessProteome preprocesses proteome data stored in a SummarizedExperiment object by performing filtering, transformation, normalization, imputation, and batch effect removal.

Usage

preprocessProteome(
  seData,
  filterList = NULL,
  missCut = 50,
  transform = c("log2", "vst", "none"),
  normalize = FALSE,
  getPP = FALSE,
  removeOutlier = NULL,
  impute = c("none", "QRILC", "MLE", "bpca", "missForest", "MinDet"),
  batch = NULL,
  verbose = FALSE,
  scaleFactorTab = NULL
)

Arguments

seData

A SummarizedExperiment object containing proteome data.

filterList

A list of filters to apply on the samples. Default is NULL.

missCut

Numeric value specifying the missing value cutoff percentage for filtering features. Default is 50.

transform

Character string specifying the transformation method ("log2", "vst", "none"). Default is "log2".

normalize

Logical value indicating whether to normalize the data. Default is FALSE.

getPP

Logical value indicating whether to retrieve PP samples. Default is FALSE.

removeOutlier

Character vector of samples to be removed as outliers. Default is NULL.

impute

Character string specifying the imputation method ("QRILC", "MLE", "bpca", "missForest", "MinDet", "none"). Default is "none".

batch

Character vector specifying batch effects to remove. Default is NULL.

verbose

Logical value indicating whether to print detailed information. Default is FALSE.

scaleFactorTab

Data frame containing scale factors for normalization. Default is NULL.

Value

A SummarizedExperiment object with preprocessed proteome data.

Examples

library(SummarizedExperiment)
# Load multiAssayExperiment object
data("dia_example")
# Get SummarizedExperiment object
se <- dia_example[["Proteome"]]
colData(se) <- colData(dia_example)
# Call the function
preprocessProteome(seData = se, normalize = TRUE, impute = "QRILC")
#> Imputing along margin 2 (samples/columns).
#> class: SummarizedExperiment 
#> dim: 491 27 
#> metadata(0):
#> assays(2): Intensity imputed
#> rownames(491): p1 p2 ... p499 p500
#> rowData names(2): UniprotID Gene
#> colnames(27): FullProteome_1stCrtl_0min_rep2
#>   FullProteome_1stCrtl_0min_rep3 ... FullProteome_HGF_24h_rep1
#>   FullProteome_HGF_100min_rep1
#> colData names(6): sample treatment ... sampleType sampleName