get_aligned_seq_for_mea: Taking S/T/Y as the center, align sequence to fasta library...

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

Taking S/T/Y as the center, align sequence to fasta library by the specific length.

Description

Taking S/T/Y as the center, align sequence to fasta library by the specific length.

Usage

get_aligned_seq_for_mea(
  ID,
  Sequence,
  AA_in_protein,
  fixed_length,
  species = "human",
  fasta_type = "refseq"
)

Arguments

ID	A vector for gi number of proteins.
Sequence	A vector for sequence of peptides.
AA_in_protein	A vector for the locations of S/T/Y in sequence of proteins.
fixed_length	Length of aligned sequence,the default is 15.
species	A string for the library of species, 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 data frame containing ID, Sequence, AA_in_protein, aligned_seq.

Author(s)

Dongdong Zhan and Mengsha Tong

References

Hadley Wickham (2018). stringr: Simple, Consistent Wrappers for Common String Operations. R package version 1.3.0.\ https://CRAN.R-project.org/package=stringr.

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_aligned_seq_for_mea.RData"
load_data <- load_data_with_ftp(ftp_url, 'RData')
writeBin(load_data, "get_aligned_seq_for_mea.RData")
load("get_aligned_seq_for_mea.RData")

foreground_df <- get_aligned_seq_for_mea(
  ID[1:100], Sequence[1:100], AA_in_protein[1:100],
  fixed_length, species = 'human',
  fasta_type = 'refseq'
)
head(foreground_df)

}

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