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Import a mzTab-M 2.1 file

Source: R/import.R
MzTabM-import.Rd

Reads and parses an mzTab-M (version 2.1) file into a MzTabM object.

The parser recognises the four standard sections:

  • MTD (Metadata): Always required. The metadata section provides additional information about the dataset(s) reported in the mzTab-M 2.1 file.

  • SML (Small Molecule Summary): Optional. Each row of the small molecule section is intended to report one final result to be communicated in terms of a molecule that has been quantified.

  • SMF (Small Molecule Feature): Optional but required when the SME section is present. The small molecule feature section represents individual MS regions that have been measured/quantified. Each SMF row SHOULD represent a single isotopomer.

  • SME (Small Molecule Evidence): Optional. The small molecule evidence section represents evidence for identifications of small molecules/features. In a typical case, each row represents one result from a single search or intepretation of a piece of evidence.

Section headers (SMH, SFH, SEH) are used as column names for their respective data sections. The MTD section does not have a dedicated header row; its two-column key–value structure is returned without column names.

Usage

readMzTabM(path, validate = TRUE, ...)

Arguments

path

character(1) with the path to the mzTab-M file.

validate

logical(1) to run the validation on the file. Default: TRUE.

...

Additional arguments forwarded to every internal call to data.table::fread.

Value

A MzTabM object containing between one and four elements, depending on which sections are present in the file:

  • MTD: A matrix with two columns. Column names are absent (the prefix column is dropped).

  • SML: A matrix whose column names are taken from the SMH header row. Present only when SMH is found in the file.

  • SMF: A matrix whose column names are taken from the SFH header row. Present only when SFH is found in the file.

  • SME: A matrix whose column names are taken from the SEH header row. Present only when both SFH and SEH are found in the file.

Author

Gabriele Tomè

Examples


## Basic usage
result <- readMzTabM(system.file("example_mztabm","MTBLS8735_mtd_smf.mzTab",
                                   package = "RmzTabM"))
#> Validation finished successfully: 2 message(s) found, including:
#> 	- Info(s): 2
#> 	- Warning(s): 0
#> 	- Error(s): 0
#> 
#> Validation messages:
#>   level code line_no
#> 1  Info 2057      -1
#> 2  Info 2057      -1
#>                                                                                                                                           text
#> 1 "small_molecule-quantification_unit" is present but the profile "M+F" has no "small molecule summary (SML)" section that would require it.\r
#> 2                          "database" is present but the profile "M+F" has no "small molecule evidence (SME)" section that would require it.\r
result
#> Object of class MzTabM
#> mzTab-M version 2.1.0-M
#>  MTD section with 203 rows.
#>  SMF section with 9068 rows and 22 columns.

## Read without validation
result <- readMzTabM(system.file("example_mztabm","MTBLS8735_mtd_smf.mzTab",
                                   package = "RmzTabM"),
                     validate = FALSE)
result
#> Object of class MzTabM
#> mzTab-M version 2.1.0-M
#>  MTD section with 203 rows.
#>  SMF section with 9068 rows and 22 columns.