Read proteomics data into a pepdiff_data object

Imports a CSV file containing PRM proteomics data and creates a pepdiff_data object suitable for analysis with [compare()].

Usage

read_pepdiff(file, id, gene, value, factors, replicate, tech_rep = NULL)

Arguments

file: Path to CSV file
id: Column name containing peptide identifiers
gene: Column name containing gene identifiers
value: Column name containing abundance values
factors: Character vector of column names to use as experimental factors
replicate: Column name containing biological replicate identifiers
tech_rep: Optional column name containing technical replicate identifiers. If provided, data will NOT be automatically combined - use [combine_tech_reps()] explicitly after import.

Value

A pepdiff_data object with components:

data: Tibble with columns: peptide, gene_id, [factors], bio_rep, value
factors: Character vector of factor names
design: Tibble of factor combinations with n_reps, n_peptides
missingness: Tibble of peptide missingness statistics
peptides: Character vector of unique peptide IDs
call: The original function call

Examples

if (FALSE) { # \dontrun{
# Simple import with one factor
dat <- read_pepdiff(
  "data.csv",
  id = "peptide_sequence",
  gene = "gene_name",
  value = "intensity",
  factors = "treatment",
  replicate = "bio_rep"
)

# Multi-factor import
dat <- read_pepdiff(
  "data.csv",
  id = "peptide",
  gene = "gene_id",
  value = "total_area",
  factors = c("treatment", "timepoint"),
  replicate = "bio_rep"
)
} # }