ID_match {DDPNA}R Documentation

homolog protein Uniprot ID transformation

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:https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ If unstall 'blast+' software, it could use R function replaced, but it will take a lot of time. 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

# suggested to install blast+ software

# it will take a long time without blast+ software
data(Sample_ID_data)
if(requireNamespace("Biostrings", quietly = TRUE)){
  out.folder = tempdir();
  write.table(Sample_ID_data$db1,file.path(out.folder,"db1.fasta"),
              quote = FALSE,row.names = FALSE, col.names = FALSE);
  write.table(Sample_ID_data$db2,file.path(out.folder,"db2.fasta"),
              quote = FALSE,row.names = FALSE, col.names = FALSE);
  data <- ID_match(Sample_ID_data$ID_match_data,
                   db1.path = file.path(out.folder,"db1.fasta"),
                   db2.path = file.path(out.folder,"db2.fasta"),
                   out.folder = out.folder,
                   blast.path = NULL,
                   evalue = 0.1, verbose = 1)
 file.remove( file.path(out.folder,"db1.fasta"),
              file.path(out.folder,"db2.fasta"))
}


[Package DDPNA version 0.3.1 Index]