MaxQdataconvert {DDPNA}

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

See Also

ID_match

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") )
  }