pre_process_filter_psites: Get peptides data frame passed phosphorylation sites quality...

In ecnuzdd/PhosMap: A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data

Get peptides data frame passed phosphorylation sites quality control.

Description

Filter phosphorylation sites by extracting all peptides with ion score>=20 and FDR<0.01 from Firmiana and having psites scores. Generate new IDs consisting of sequence, gi, psite. Quantification values containing area and psm.

Usage

pre_process_filter_psites(
  firmiana_peptide_dir,
  psites_score_dir,
  phospho_experiment_design_file_path,
  qc,
  min_score = 20,
  min_FDR = 0.01
)

Arguments

firmiana_peptide_dir	A folder containing peptide identification files from Firmiana as input.
psites_score_dir	A folder containing psites scores files extracted from mascot xml as input.
phospho_experiment_design_file_path	A string representing the path of phospho-experiment design file as input.
qc	A boolean value representing whether it has QC files. The default is True.
min_score	A numeric for the minimum score of credible peptides, the default is 20 for Mascot ion score.
min_FDR	A numeric for the minimum FDR of credible peptides, the default is 0.01.

Value

A merged data frame containing sequence, gi, psite, area and psm.

Examples

## Not run: 
merge_df_with_phospho_peptides <- pre_process_filter_psites(
  firmiana_peptide_dir,
  psites_score_dir
)

## End(Not run)

ecnuzdd/PhosMap documentation built on Dec. 7, 2022, 4:09 a.m.