get_modification_index: Get indexes of modifications in protein sequences.

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

Get indexes of modifications in protein sequences.

Description

Get indexes of modifications in protein sequences.

Usage

get_modification_index(id_data_only_peptide2gi, fasta_data)

Arguments

id_data_only_peptide2gi	a data frame for peptides with protein gi.
fasta_data	a fasta data for a specific species.

Value

A vector for indexes of modifications in protein sequences.

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_modification_index.RData"
load_data <- load_data_with_ftp(ftp_url, 'RData')
writeBin(load_data, "get_modification_index.RData")
load("get_modification_index.RData")

modification_index_in_protein_seq_list <- get_modification_index(
  id_data_only_peptide2gi[1:100, ],
  fasta_data
)
head(modification_index_in_protein_seq_list)
}

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