MzTabReader-class: Class to read an mzTab file and store the tables internally.

Description

The 'sections' field is initialized after $readMzTab was called. The 'fn_map' fields should be initialized via ...$fn_map$readMappingFile(...) manually if user-defined filename mappings are desired and is automatically updated/queried when $readMzTab is called.

Arguments

Fields

sections: MzTab sections as list. Valid list entries are: "MTD", "PRT", "PEP", "PSM", "SML", "filename" and "comments"

fn_map

FilenameMapper which can translate raw filenames into something shorter

Methods

getEvidence(): Basically the PSM table and additionally columns named 'raw.file' and 'fc.raw.file'.

getMSMSScans(identified_only = FALSE)

Basically the PSM table (partially renamed columns) and additionally two columns 'raw.file' and 'fc.raw.file'. If identified_only is TRUE, only MS2 scans which were identified (i.e. a PSM) are returned -- this is equivalent to msms.txt in MaxQuant.

getParameters()

Converts internal mzTab metadata section to a two column key-value data.frame similar to MaxQuants parameters.txt.

getProteins()

Basically the PRT table ...

getSummary()

Converts internal mzTab metadata section to a two data.frame with columns 'fc.raw.file', 'ms.ms.identified....' similar to MaxQuants summary.txt.

renameColumns(dt, namelist)

Renames all columns and throws a warning if a column does not exist in the data

RTUnitCorrection(dt)

Convert all RT columns from seconds (OpenMS default) to minutes (MaxQuant default)