Global FDR estimation

Global FDR estimation

Input PSM file

The input PSM file must be in TSV format and the following columns are required:

• index: Spectrum ID
• peptide: Peptide sequence
• charge: Precursor charge
• score: The score of PSM
• protein: Multiple protein IDs are separated by ";"

Example

PSM level FDR estimation

library(PGA)
calculateFDR(psmfile="all_psm.txt",
             db="db.fasta",
             fdr=0.01,
             decoyPrefix="XXX_",
             better_score_lower=TRUE,
             remap=FALSE,
             out_dir="./",
             protein_inference=FALSE,
             xmx=4)

Set parameter protein_inference as TRUE to perform protein inference.

Peptide level FDR estimation

library(PGA)
calculateFDR(psmfile="all_psm.txt",
             db="db.fasta",
             peptide_level=TRUE,
             fdr=0.01,
             decoyPrefix="XXX_",
             better_score_lower=TRUE,
             remap=FALSE,
             out_dir="./",
             protein_inference=FALSE,
             xmx=4)