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

In PTXQC: Quality Report Generation for MaxQuant and mzTab Results

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.

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

RTUnitCorrection(dt)

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

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

PTXQC documentation built on May 29, 2024, 9:26 a.m.