Load spike-in proteomics data into a SummarizedExperiment

Usage

load_spike_data(
  data,
  md,
  spike_column,
  spike_value,
  spike_concentration,
  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)
spike_column: name of the column specifying which proteins are the spike-ins
spike_value: String value specifying the spike-in proteins in the spike-in column
spike_concentration: name of the column in md defining the spike-in concentration per sample
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("Ecoli_human_MaxLFQ_protein_intensities.csv")
md_path <- readPRONE_example("Ecoli_human_MaxLFQ_metadata.csv")
data <- read.csv(data_path)
md <- read.csv(md_path)
mixed <- grepl("Homo sapiens.*Escherichia|Escherichia.*Homo sapiens", data$Fasta.headers)
data <- data[!mixed,]
data$Spiked <- rep("HUMAN", nrow(data))
data$Spiked[grepl("ECOLI", data$Fasta.headers)] <- "ECOLI"
se <- load_spike_data(data, md, spike_column = "Spiked", spike_value = "ECOLI", 
        spike_concentration = "Concentration", protein_column = "Protein.IDs", 
        gene_column = "Gene.names", ref_samples = NULL, batch_column = NULL, 
        condition_column = "Condition", label_column = "Label")