get_df_with_AAs_i: Get a data frame of amino acid sequences for proteins.

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

Get a data frame of amino acid sequences for proteins.

Description

Get a data frame of amino acid sequences for proteins.

Usage

get_df_with_AAs_i(
  unique_proteins,
  i,
  id_data_only_peptide2gi,
  proteins_in_id_data_only_peptide2gi,
  sequences_in_id_data_only_peptide2gi,
  modification_index_in_protein_seq_list
)

Arguments

unique_proteins	a vector for unique proteins.
i	the ith unique proteins.
id_data_only_peptide2gi	a data frame for peptides with protein gi.
proteins_in_id_data_only_peptide2gi	a vector for proteins with only protein gi.
sequences_in_id_data_only_peptide2gi	a vector for peptides with only protein gi.
modification_index_in_protein_seq_list	a list for the index of modifications in protein sequence.

Value

A data frame with sequences for proteins.

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_df_with_AAs_i.RData"
load_data <- load_data_with_ftp(ftp_url, 'RData')
writeBin(load_data, "get_df_with_AAs_i.RData")
load("get_df_with_AAs_i.RData")

df_with_AAs_i <- get_df_with_AAs_i(unique_proteins, i,
  id_data_only_peptide2gi,
  proteins_in_id_data_only_peptide2gi,
  sequences_in_id_data_only_peptide2gi,
  modification_index_in_protein_seq_list
)
head(df_with_AAs_i)
}

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