MaxquantDataconvert: one-step to extract Maxquant quantification data and convert

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

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: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.

Author(s)

Kefu Liu

See Also

ID_match

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.
out.folder = "C:/DDPNA_test/";
blast.path = "C:/blast/ncbi-blast-2.7.1+/bin/";
pgfilename = "C:/DDPNA_test/Sample_protein_groups.txt"
if (file.exists(pgfilename) & file.exists(out.folder) & dir.exists(blast.path))
  Maxdata <- MaxQdataconvert(pgfilename, IDtype = "MaxQ",
                             db1.path = "C:/DDPNA_test/new.fasta",
                             db2.path = "C:/DDPNA_test/ori.fasta",
                             out.folder = out.folder,
                             blast.path = blast.path)

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