MSnIDFilter-class: The "MSnIDFilter" Class for Handling MS/MS Criteria,...

In MSnID: Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

Description

The MSnIDFilter is a convenience class for manipulating the MS/MS filter for MS/MS results.

Objects from the Class

The way to create objects is to call MSnIDFilter constructor function that takes as input the MSnID class instance and (optionally) filterList.

Slots

MSnIDObj:

An instance of class "MSnID".

filterList:

An optional argument. A list with element names corresponding to column names avalable in MSnID instance. Each element contains sub-elements "comparison" and "threshold". "Comparison" is one of the relationship operators (e.g. ">") see Comparison for details. "Threshold" is the corresponding parameter value the identification has to be more or less (depending on comparison) to pass the filter.

Methods

show

signature(object="MSnIDFilter"):
Prints MSnIDFilter object.

object$name, object$name<-value

Access and set filterList elements.

names

signature(x="MSnIDFilter")
Returns the names of the criteria.

as.numeric

signature(x="MSnIDFilter")
Converts filterList into "numeric" vector. Vector names are the list element names. Vector values are threshold values. Comparison operators are lost.

length

signature(x="MSnIDFilter")
Returns the number of criteria set in the "MSnIDFilter" object.

update

signature(object="MSnIDFilter", ...)
The additional ... argument is numeric vector of the same length as the number of criteria in MSnIDFilter object. The method update the corresponding thresholds to new provided values.

Author(s)

Vladislav A Petyuk [e-mail]

See Also

MSnSet evaluate_filter apply_filter optimize_filter

Examples

data(c_elegans)

## Filtering using filter object:
# first adding columns that will be used as filters
msnidObj$msmsScore <- -log10(msnidObj$`MS-GF:SpecEValue`)
msnidObj$mzError <- abs(msnidObj$experimentalMassToCharge - 
                        msnidObj$calculatedMassToCharge)
# setting up filter object
filtObj <- MSnIDFilter(msnidObj)
filtObj$msmsScore <- list(comparison=">", threshold=10.0)
filtObj$mzError <- list(comparison="<", threshold=0.1) # 0.1 Thomson
show(filtObj)
# applying filter and comparing MSnID object before and after
show(msnidObj)
msnidObj <- apply_filter(msnidObj, filtObj)
show(msnidObj)

MSnID documentation built on Nov. 8, 2020, 8:03 p.m.