Description Objects from the Class Slots Methods Author(s) See Also Examples
The MSnIDFilter
is a convenience class for manipulating the MS/MS
filter for MS/MS results.
The way to create objects is to call MSnIDFilter
constructor function that takes as input the MSnID
class instance and (optionally) filterList
.
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.
signature(object="MSnIDFilter")
:
Prints MSnIDFilter
object.
object$name
, object$name<-value
Access and set filterList elements.
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.
Vladislav A Petyuk vladislav.petyuk@pnnl.gov
MSnSet
evaluate_filter
apply_filter
optimize_filter
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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)
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