get_summary_with_unique_sites: Assign psites to protein sequence.

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

Assign psites to protein sequence.

Description

Construct the data frame with unique phosphorylation site for each protein sequence and eliminate redundancy.

Usage

get_summary_with_unique_sites(
  combined_df_with_mapped_gene_symbol,
  species = "human",
  fasta_type = "refseq"
)

Arguments

combined_df_with_mapped_gene_symbol	A dataframe with Sequence, ID, Modification, Gene Symbol, Area and PSMs as input.
species	A string, the options are human, mouse and rattus, the default is human.
fasta_type,	A string for fasta source, the options are refseq and uniprot, the default is refseq

Value

A dataframe that all redundant psites are assigned to protein sequence.

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_summary_with_unique_sites.RData"
load_data <- load_data_with_ftp(ftp_url, 'RData')
writeBin(load_data, "get_summary_with_unique_sites.RData")
load("get_summary_with_unique_sites.RData")

summary_df_of_unique_proteins_with_sites <- get_summary_with_unique_sites(
  combined_df_with_mapped_gene_symbol[1:100, ],
  species = 'human',
  fasta_type = 'refseq'
)
head(summary_df_of_unique_proteins_with_sites)

}

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