Load real-world proteomics data into a SummarizedExperiment

Usage

load_data(
  data,
  md,
  protein_column = "Protein.IDs",
  gene_column = "Gene.Names",
  ref_samples = NULL,
  batch_column = NULL,
  condition_column = NULL,
  label_column = NULL
)

Arguments

data: tabular data table with rows = proteins and columns = samples (such as proteinGroups.txt of MaxQuant)
md: experimental design table (requires a column named "Column" for the column names of the sample intensities in data)
protein_column: name of the column in data containing the protein IDs
gene_column: name of the column in data containing the gene names
ref_samples: reference samples if TMT experiment provided (names of samples)
batch_column: name of the column in md defining the batches
condition_column: name of the column in md defining the condition (can still be changed afterwards)
label_column: name of the column in md containing simple sample names (for visualization)

Value

SummarizedExperiment object

Examples

data_path <- readPRONE_example("tuberculosis_protein_intensities.csv")
md_path <- readPRONE_example("tuberculosis_metadata.csv")
data <- read.csv(data_path)
md <- read.csv(md_path)
md$Column <- stringr::str_replace_all(md$Column, " ", ".")
ref_samples <- md[md$Group == "ref",]$Column
se <- load_data(data, md, protein_column = "Protein.IDs",
               gene_column = "Gene.names", ref_samples = ref_samples,
               batch_column = "Pool", condition_column = "Group",
               label_column = "Label")