get_list_with_filtered_sites: Filter phosphorylation sites.

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

Filter phosphorylation sites.

Description

Filter phosphorylation sites by extracting all peptides with ion score>=20 and FDR<0.01 from Firmiana and having psites scores.

Usage

get_list_with_filtered_sites(
  peptide_id,
  files,
  files_site_score,
  qc,
  min_score,
  min_FDR
)

Arguments

peptide_id	A vector containing experiment ids as input.
files	A data list containing peptides identificaton from Firmiana as input.
files_site_score	A data list containing psites scores extracted from mascot xml. The default is NULL, which represents no QC file.
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 list containing peptides dataframe with area values and psm, IDs with mergered sequences, gi and sites, new peptides dataframe combined previous peptides dataframe and IDs.

Author(s)

Dongdong Zhan and Mengsha Tong

Examples

## Not run: 
result_list_with_filtered_sites <- get_list_with_filted_sites(
  peptide.id,
  files,
  files_site_score
)

## End(Not run)

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