get_normalized_data_of_psites: To normalize data and filter data only including...

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

To normalize data and filter data only including phosphorylation sites.

Description

To normalize data and filter data only including phosphorylation sites.

Usage

get_normalized_data_of_psites(
  data_frame,
  experiment_code_file_path,
  topN = NA,
  mod_types = c("S", "T", "Y")
)

Arguments

data_frame	A data frame containing IDs and quantification values merged from multi-experiments as input.
experiment_code_file_path	A file path of storing experiment codes as input. The experiment codes are required to keep pace with column names of Value.
topN,	A numeric value, selecting N p-sites with high intensity rank for normalization, the default is NA.
mod_types,	A vector for modification residues, the default is c('S', 'T', 'Y') for phosphorylation modifications.

Value

A list including data frame after filtering or normalization (x 1e5).

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/get_normalized_data_of_psites.RData"
ftp_url2 <- "ftp://111.198.139.72:4000/pub/PhosMap_datasets/function_demo_data/phosphorylation_exp_design_info.txt"
load_data1 <- load_data_with_ftp(ftp_url1, 'Rdata')
writeBin(load_data1, "get_normalized_data_of_psites.RData")
load("get_normalized_data_of_psites.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"

phospho_data_filtering_STY_and_normalization_list <- get_normalized_data_of_psites(
  summary_df_of_unique_proteins_with_sites,
  phosphorylation_exp_design_info_file_path,
  topN = NA, mod_types = c('S', 'T', 'Y')
)
head(phospho_data_filtering_STY_and_normalization_list)

}

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