get_combined_data_frame: Get a data frame mapped ID to Gene Symbol.

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

Get a data frame mapped ID to Gene Symbol.

Description

This is an intermediate file and a dataframe with Gene Symbol exported. Based on a library file consisting of mapping relationships about Gene Symbol, GeneID, RefSeq_Protein_GI, RefSeq_Protein_Accession and Uniprot_Protein_Accession, a new dataframe with Sequence, GI, Modification, Gene Symbol, Area and PSMs,is contructed.

Usage

get_combined_data_frame(
  merge_df_with_phospho_peptides,
  species = "human",
  id_type = "RefSeq_Protein_GI"
)

Arguments

merge_df_with_phospho_peptides	A dataframe consisting of IDs (Sequence_GI_Psite) and Area values.
species	A string, the options are human, mouse and rattus, the default is human.
id_type	A string, the options are 'GeneID', 'RefSeq_Protein_GI', 'RefSeq_Protein_Accession' and 'Uniprot_Protein_Accession', the default is RefSeq_Protein_GI.

Value

A dataframe with Sequence, GI, Modification, Gene Symbol, Area values and PSMs

Author(s)

Dongdong Zhan and Mengsha Tong

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_url <- "ftp://111.198.139.72:4000/pub/PhosMap_datasets/function_demo_data/get_combined_data_frame.RData"
    load_data <- load_data_with_ftp(ftp_url, 'RData')
    writeBin(load_data, "get_combined_data_frame.RData")
    load("get_combined_data_frame.RData")

    combined_df_with_mapped_gene_symbol <- get_combined_data_frame(
      merge_df_with_phospho_peptides[1:11,], species = 'human',
      id_type = 'RefSeq_Protein_GI'
    )
    head(combined_df_with_mapped_gene_symbol)
}

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