qc_maxquant: Quality control for phosphoproteomics data from MaxQuant.

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

Quality control for phosphoproteomics data from MaxQuant.

Description

Quality control for phosphoproteomics data from MaxQuant.

Usage

qc_maxquant(
  data_frame,
  experiment_code_file_path,
  min_score = 40,
  min_loc_prob = 0.75,
  max_na_num = 2
)

Arguments

data_frame	A data frame of Phospho (STY)Sites.txt.
experiment_code_file_path	Experiment code file path.
min_score	Threshold for MaxQuant score. The default is 40.
min_loc_prob	Threshold for MaxQuant Localization.prob. The default is 0.75.
max_na_num	Threshold for the number of missing values. The default is 2.

Value

A result list. Elements are a data frame containing quality control result and a data frame containing information required for motif analysis.

Examples

## Not run: 
rawdata <- read.csv("Phospho (STY)Sites.txt",header=T,sep='\t')
qc_results <- qc_maxquant(rawdata, "./experiment_code_file.txt", min_score = 40, min_loc_prob = 0.75, max_na_num = 2)
qc_result <- qc_results[[1]]
qc_result_for_motifanalysis <- qc_results[[2]]

## End(Not run)

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