mzIDevidence-class: A class to store peptide evidence information from an...

Description Usage Arguments Details Methods (by generic) Slots Objects from the class See Also

Description

This class handles parsing and storage of peptide evidence information from mzIDentML files, residing at the /*/x:SequenceCollection/x:PeptideEvidence node.

Usage

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## S4 method for signature 'mzIDevidence'
show(object)

## S4 method for signature 'mzIDevidence'
length(x)

## S4 method for signature 'mzIDevidence'
evidence(object, safeNames = TRUE)

Arguments

object

An mzIDevidence object

x

An mzIDevidence object

safeNames

Should column names be lowercased to ensure compatibility between v1.0 and v1.1 files?

Details

The content of the class is stored in a data.frame with columns depending on the content of the mzIdentML file. Columns represent the attribute values of for each PeptideEvidence node. For files conforming to the HUPO standard, dbSequence_ref, id and peptide_ref is required while start, end, pre, post, name, isDecoy, frame and translationTable_ref are optional. Information residing in cvParam and userParam children are not parsed.

Methods (by generic)

Slots

evidence

A data.frame containing all peptide evidence from the mzIdentML file

Objects from the class

Objects of mzIDevidence are not meant to be created explicitly but as part of the mzID-class. Still object can be created with the constructor mzIDevidence.

See Also

mzIDevidence

Other mzID.classes: mzID-class, mzIDCollection-class, mzIDdatabase-class, mzIDparameters-class, mzIDpeptides-class, mzIDpsm-class


thomasp85/mzID documentation built on May 31, 2019, 11:14 a.m.