normalize_phos_data_to_profiling: Normalize phospho-data to profiling

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

Normalize phospho-data to profiling

Description

Normalize phospho-data to profiling

Usage

normalize_phos_data_to_profiling(
  phospho_data_normalized,
  profiling_data_normalized,
  phosphorylation_exp_design_info_file_path,
  profiling_exp_design_info_file_path,
  control_label = NA,
  pair_flag = FALSE
)

Arguments

phospho_data_normalized	A data frame of phospho-data after normalization
profiling_data_normalized	A data frame of profiling after normalization
phosphorylation_exp_design_info_file_path	A file path about phosphorylation experiment design, it has 2 kinds of file configuration as follows: 1. experiment_design_noPair.txt must contain columns of Experiment_Code, Group. 2. experiment_design_Pair.txt must contain columns of Experiment_Code, Group, and Pair. (Pair: 1 -> case, -1 -> control)
profiling_exp_design_info_file_path	A file path about profiling experiment design, it has 2 kinds of file configuration as same as phosphorylation_exp_design_info_file_path.
control_label	A string represents label of control group. The default is NA which shows no control group.
pair_flag	A boolean value represents whether experiments have pairs. The default is FALSE which shows no pairs.

Value

A data frame which comes from results that phospho-data is normalizated base on the abundance of proteins in the profiling experiments.

Examples

## The process needs to load data from PhosMap datasets stored into FTP server and perform large computation.
## It may take a few minutes.
if(FALSE){
    ftp_url1 <- "ftp://111.198.139.72:4000/pub/PhosMap_datasets/function_demo_data/normalize_phos_data_to_profiling.RData"
    ftp_url2 <- "ftp://111.198.139.72:4000/pub/PhosMap_datasets/function_demo_data/phosphorylation_exp_design_info.txt"
    ftp_url3 <- "ftp://111.198.139.72:4000/pub/PhosMap_datasets/function_demo_data/profiling_exp_design_info.txt"

    load_data1 <- load_data_with_ftp(ftp_url1, 'Rdata')
    writeBin(load_data1, "normalize_phos_data_to_profiling.RData")
    load("normalize_phos_data_to_profiling.RData")

    load_data2 <- load_data_with_ftp(ftp_url2, 'downloadtxt')
    writeBin(load_data2, "phosphorylation_exp_design_info.txt")
    phosphorylation_exp_design_info_file_path <- "./phosphorylation_exp_design_info.txt"

    load_data3 <- load_data_with_ftp(ftp_url3, 'downloadtxt')
    writeBin(load_data3, "profiling_exp_design_info.txt")
    profiling_exp_design_info_file_path <- "./profiling_exp_design_info.txt"

    data_frame_normalization_with_control_no_pair <- normalize_phos_data_to_profiling(
      phospho_data_topX, profiling_data_normalized,
      phosphorylation_exp_design_info_file_path,
      profiling_exp_design_info_file_path,
      control_label = '0',
      pair_flag = FALSE
    )
    head(data_frame_normalization_with_control_no_pair)
}

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