ID_match: homolog protein Uniprot ID transformation

In liukf10/TEST: Disease-Drived Differential Proteins and Proteome-Wide Co-Expression Network Associated Analysis

Description

homolog protein Uniprot ID match

Usage

ID_match(data, db1.path = NULL, db2.path = NULL,out.folder = NULL,
         blast.path = NULL,evalue = 0.1, verbose = 1)

Arguments

data	dataset of protein information.Column Names should contain "ori.ID" and "ENTRY.NAME". "ori.ID" is Uniprot ID
db1.path	fasta file, database of transfered species
db2.path	fasta file, database of original species
out.folder	blast result output folder, the folder path should be the same with db1.path
blast.path	blast+ software install path
evalue	blast threshold, the lower means more rigorous
verbose	integer level of verbosity. Zero means silent, 1 means have Diagnostic Messages.

Details

homolog protein Uniprot ID match is based on the ENTRY.NAME, gene name and sequence homophyly in two different species or different version of database.

Value

a data.frame included 4 columns: ori.ID, ENTRY.NAME, new.ID, match.type.

Note

This function should install blast+ software, Version 2.7.1. blast+ download website:ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ db1.path, db2.path, out.folder are both need the complete path. Out.folder and db1.path should be in the same folder. Path should have no special character. data should have colname: ori.ID, ENTRY.NAME.

Author(s)

Kefu Liu

Examples

rm(list = ls())

library(DDPNA)
#database file should be downloaded and extracted the rar file in C Disk.
#blast+ software should be downloaded and installed in C Disk.
#the example file should be downloaded and decompress in C Disk.
data(Sample_ID_data)
# need to install blast+ software
out.folder = "C:/DDPNA_test/";
blast.path = "C:/blast/ncbi-blast-2.7.1+/bin/";
if(file.exists(out.folder) & dir.exists(blast.path))
  data <- ID_match(ID_data,
                   db1.path = "C:/DDPNA_test/new.fasta",
                   db2.path = "C:/DDPNA_test/ori.fasta",
                   out.folder = out.folder,
                   blast.path = blast.path,
                   evalue = 0.1, verbose = 1)

liukf10/TEST documentation built on May 20, 2019, 12:59 a.m.