Adjust Protein Expression

This function adjusts the glycopeptide expression by the protein expression. In another word, it "strips out" the protein expression from the glycopeptide expression, so that the expression reflects the glycosylation status only.

Usage

adjust_protein(exp, pro_expr_mat, method = c("ratio", "reg"))

Arguments

exp

A glyexp_experiment object containing glycoproteomics data.

pro_expr_mat

A matrix of protein expression. Columns are samples, rows are uniprot protein accessions.

method

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

Value

A glyexp_experiment object with adjusted protein expression.

Details

For simplicity, glycopeptide expression is denoted as GP, and protein expression is denoted as PRO.

"ratio" method

GP-adj = (GP / PRO) / (median(GP) / median(PRO))

The first part is to adjust glycopeptide expression by protein expression. The second part is to rescale the expression to the original scale.

"reg" method

Use linear regression to remove the protein expression from the glycopeptide expression. Both glycopeptide and protein expression values are log2-transformed (with +1 to avoid log(0)) before fitting the linear model: log2(GP+1) ~ log2(PRO+1). The residuals represent the glycosylation-specific signal and are converted back to the original scale using 2^residuals, ensuring all adjusted values are positive.

In both methods, only glycoproteins identified in both exp and pro_expr_mat will be retained.