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Step: Adjust Protein Abundance

step_adjust_protein.Rd

Adjust glycoform quantification values by correcting for protein abundance utilizing glyclean::adjust_protein(). Usually this step should be run after step_preprocess().

Usage

step_adjust_protein(pro_expr_path = NULL, method = "ratio")

Arguments

pro_expr_path

Path to the protein expression matrix file. If NULL, this step will be skipped. Can be:

  • A CSV/TSV file with the first column as protein accessions and remaining columns as sample names.

  • An RDS file with a matrix or data.frame with row names as protein accessions and columns as sample names.

method

The method to use for protein adjustment. Either "ratio" or "reg". Default is "ratio".

Value

A glysmith_step object.

Details

Data required:

  • exp: The experiment to adjust

Data generated:

  • unadj_exp: The original experiment (previous exp, saved for reference)

This step is special in that it silently overwrites the exp data with the adjusted experiment. This ensures that no matter if adjustment is performed or not, the "active" experiment is always under the key exp. The previous exp is saved as unadj_exp for reference.

AI Prompt

This section is for AI in inquire_blueprint() only.

  • Include this step only if the user explicitly asks for protein adjustment.

  • If protein adjustment is needed and the pro_expr_path is not provided, ask for it and explain how to prepare the file:

    • CSV/TSV: first column is protein accessions; remaining columns are sample names.

    • RDS: a matrix/data.frame with row names as protein accessions and columns as sample names.

  • You MUST provide a detailed explanation of how to prepare the file.

  • With out the file, the step is invalid.

See also

glyclean::adjust_protein()

Examples

fake_pro_expr_mat <- matrix(rnorm(100), nrow = 10, ncol = 10)
rownames(fake_pro_expr_mat) <- paste0("P", seq_len(10))
colnames(fake_pro_expr_mat) <- paste0("S", seq_len(10))
fake_pro_expr_path <- tempfile(fileext = ".rds")
saveRDS(fake_pro_expr_mat, fake_pro_expr_path)
step_adjust_protein(fake_pro_expr_path)
#> <step "step_adjust_protein(pro_expr_path = fake_pro_expr_path)"> Protein
#> adjustment