MaxquantDataconvert: one-step to extract 'Maxquant' quantification data and...
In DDPNA: Disease-Drived Differential Proteins Co-Expression Network Analysis

MaxQdataconvert

R Documentation

one-step to extract 'Maxquant' quantification data and convert

Description

'Maxquant' quantification data extract and homolog protein Uniprot ID match.

Usage

MaxQdataconvert(pgfilename, IDname = "Majority.protein.IDs",
                IDtype = c("MaxQ","none"), CONremove = TRUE,
                justID = TRUE, status1 = TRUE, ENTRY1 = TRUE,
                db1.path = NULL, db2.path = NULL,
                out.folder = NULL, blast.path = NULL,
                savecsvpath = NULL, csvfilename = NULL,
                verbose = 1, ...)

Arguments

`pgfilename`	'Maxquant' quantification file "protein groups.txt"
`IDname`	The column name of uniprot ID. The default value is "`Majority.protein.IDs`"" which is the column name in MaxQuant data.
`IDtype`	"`MaxQ`" means `proteinGroups` is 'Maxquant' quantification data, "`none`" means other type data. This must be (an abbreviation of) one of the strings: "`MaxQ`","`none`".
`CONremove`	a logical value indicated whether remove contaminant IDs. When IDtype is "none", it will remove unmatch ID compared with database2.
`justID`	a logical value indicated whether only extract ID when IDtype is "MaxQ".
`status1`	a logical value indicated whether extract the first ID status when IDtype is "MaxQ".
`ENTRY1`	a logical value indicated whether extract the first ID ENTRY NAME when IDtype is "MaxQ".
`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
`savecsvpath`	the information of csv file name output path. The default value means don't save csv file.
`csvfilename`	the name of csv file which the data are to be output. The default value means don't save csv file.
`verbose`	integer level of verbosity. Zero means silent, higher values make the output progressively more and more verbose.
`...`	Other arguments.

Details

one-step to extract MaxQuant or other quantification data and convert. The function contain ID_match function.

Value

a list of proteomic information.

`protein_IDs`	Portein IDs which is `IDname` column information.
`intensity`	Quantification intensity informaton. When `IDtype` is "`none`", it is the `QuanCol` columns information.
`iBAQ`	Quantification iBAQ intensity informaton.(only for `IDtype` is "`MaxQ`")
`LFQ`	Quantification LFQ intensity informaton.(only for `IDtype` is "`MaxQ`")

Note

The function should install 'blast+' software, Version 2.7.1. 'blast+' download website:https://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.

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);
  write.table(Sample_ID_data$pginf,
              file = file.path(out.folder,"proteingroups.txt"),
              quote = FALSE,
              sep = "\t",dec = ".", row.names = FALSE, col.names = TRUE )
  Maxdata <- MaxQdataconvert(file.path(out.folder,"proteingroups.txt"),
                             IDtype = "MaxQ",
                             db1.path = file.path(out.folder,"db1.fasta"),
                             db2.path = file.path(out.folder,"db2.fasta"),
                             out.folder = out.folder,
                             blast.path = NULL)
  file.remove( file.path(out.folder,"db1.fasta"),
               file.path(out.folder,"db2.fasta"),
               file.path(out.folder,"proteingroups.txt") )
  }

DDPNA documentation built on May 17, 2022, 5:05 p.m.