Basic classes and methods for mass spectrometric mass list manipulation.


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Documentation for package `msbase' version 1.4.0

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A C F G H I L M N P R S U W misc

-- A --

assym,numeric-method Class "numeric"

-- C --

cals,Massvector,Massvector-method Similarity by user defined function
cals,Massvectorlist,Massvector-method Similarity by user defined function
cals,Massvectorlist,NULL-method Similarity by user defined function
cals,numeric,numeric-method Similarity by user defined function
cals-methods Similarity by user defined function
calsrange Similarity function for comparison of two peak-lists.
calssim Similarity function for comparison of two peak-lists.
coerce,ANY,numeric-method Class "numeric"
coerce,List,list-method Class "List"
coerce,Massvector,data.frame-method Class "Massvector"
coerce,Massvector,list-method Class "Massvector"
coerce,Massvector,numeric-method Class "Massvector"
coerce,Massvectorlist,data.frame-method Class "Massvectorlist"
coerce,Massvectorlist,matrix-method Class "Massvectorlist"
coerce<-,List,list-method Class "List"
col.plot,Massvectorlist-method Class "Massvectorlist"

-- F --

fbinary,list,NULL-method Binary measures for pairwise peak-list comparison
fbinary,Massvector,Massvector-method Binary measures for pairwise peak-list comparison
fbinary,Massvectorlist,Massvector-method Binary measures for pairwise peak-list comparison
fbinary,Massvectorlist,NULL-method Binary measures for pairwise peak-list comparison
fbinary,numeric,numeric-method Binary measures for pairwise peak-list comparison
fbinary-methods Binary measures for pairwise peak-list comparison
fcor,Massvector,Massvector-method Similarity measures for peak-list comparison
fcor,Massvectorlist,Massvector-method Similarity measures for peak-list comparison
fcor,Massvectorlist,NULL-method Similarity measures for peak-list comparison
fcor-methods Similarity measures for peak-list comparison
fdist,Massvector,Massvector-method Euclidean or Manhattan distance for peak-list comparison
fdist,Massvectorlist,Massvector-method Euclidean or Manhattan distance for peak-list comparison
fdist,Massvectorlist,NULL-method Euclidean or Manhattan distance for peak-list comparison
fdist-methods Euclidean or Manhattan distance for peak-list comparison
finterS,Massvector,Massvector-method Intersection of two vectors, Massvectors
finterS,Massvectorlist,Massvector-method Intersection of two vectors, Massvectors
finterS,numeric,numeric-method Intersection of two vectors, Massvectors
finterS-methods Intersection of two vectors, Massvectors
fintersect,Massvector,Massvector-method Intersection of two vectors, Massvectors
fintersect,Massvectorlist,Massvector-method Intersection of two vectors, Massvectors
fintersect,numeric,numeric-method Intersection of two vectors, Massvectors
fintersect-methods Intersection of two vectors, Massvectors
fis.element,Massvector,Massvector-method Performs *set* membership on two Massvectors
fis.element,numeric,numeric-method Performs *set* membership on two Massvectors
fis.element-methods Performs *set* membership on two Massvectors
fm,numeric-method Class "numeric"
fmatch,Massvector,Massvector-method Index of matching peaks
fmatch,numeric,numeric-method Index of matching peaks
fmatch-methods Index of matching peaks
fmatchall,Massvector,Massvector-method Index of matching and not-matching peaks
fmatchall,numeric,numeric-method Index of matching and not-matching peaks
fmatchall-methods Index of matching and not-matching peaks
fsetdiff,Massvector,Massvector-method difference
fsetdiff,Massvectorlist,Massvector-method difference
fsetdiff,numeric,numeric-method difference
fsetdiff-methods difference
fsetequal,Massvector,Massvector-method Performs *set* equality on two Massvectors
fsetequal,numeric,numeric-method Performs *set* equality on two Massvectors
fsetequal-methods Performs *set* equality on two Massvectors
funion,Massvector,Massvector-method Union of two Massvectors
funion,numeric,numeric-method Union of two Massvectors
funion-methods Union of two Massvectors

-- G --

gamasses,Massvector-method Determines clusters of masses in an Massvector
gamasses,Massvectorlist-method Determines clusters of masses in an Massvector
gamasses-methods Determines clusters of masses in an Massvector

-- H --

hg,numeric-method Class "numeric"
hist,Massvector-method Class "Massvector"
hist,Massvectorlist-method Class "Massvectorlist"

-- I --

image,Massvector-method Class "Massvector"
image,Mlist-method Class "Mlist"
initialize,Massvector-method Class "Massvector"
initialize,Massvectorlist-method Class "Massvectorlist"

-- L --

length,Massvector-method Class "Massvector"
List-class Class "List"
listdist,list-method compute object of class ``dist'' from list.
listdist-methods compute object of class ``dist'' from list.

-- M --

Massvector-class Class "Massvector"
Massvectorlist-class Class "Massvectorlist"
Mlist-class Class "Mlist"
msms.binary Transformation and other factors of the pairwise peak-lists Comparsion Process
msms.intensity Transformation and other factors of the pairwise peak-lists Comparsion Process
mvscale,Massvector-method Class "Massvector"
mvscale,Massvectorlist-method Class "Massvectorlist"

-- N --

names,Mlist-method Class "Mlist"
names<-,Mlist-method Class "Mlist"
nrmatch,Massvector,Massvector-method Number of matching peaks
nrmatch,Massvectorlist,Massvector-method Number of matching peaks
nrmatch,Massvectorlist,NULL-method Number of matching peaks
nrmatch,numeric,numeric-method Number of matching peaks
nrmatch-methods Number of matching peaks
numeric-class Class "numeric"

-- P --

pairplot,Massvector,Massvector-method Class "Massvector"
pep.plot,Massvector,missing-method Class "Massvector"
pep.plot,Massvectorlist,missing-method Class "Massvectorlist"
pldata 18 Peak-lists
plot,Massvector,Massvector-method Class "Massvector"
plot,Massvector,missing-method Class "Massvector"
plot,Massvectorlist,missing-method Class "Massvectorlist"
pmf.binary Transformation and other factors of the pairwise peak-lists Comparsion Process
pmf.intensity Transformation and other factors of the pairwise peak-lists Comparsion Process
points,Massvector-method Class "Massvector"

-- R --

readBruker,Massvector-method Class "Massvector"
readBruker,Massvectorlist-method Class "Massvectorlist"
readMV,Massvector,character-method Class "Massvector"
readMV,Massvectorlist,character-method Class "Massvectorlist"
rmi,numeric-method Class "numeric"

-- S --

show,Massvector-method Class "Massvector"
show,Massvectorlist-method Class "Massvectorlist"
subset,Mlist-method Class "Mlist"
summary,Massvector-method Class "Massvector"

-- U --

unlist,Massvectorlist-method Class "Massvectorlist"

-- W --

writeMV,Massvector,character-method Class "Massvector"
writeMV,Massvectorlist,character-method Class "Massvectorlist"

-- misc --

[,List-method Class "List"
[,Massvector-method Class "Massvector"
[,Massvectorlist-method Class "Massvectorlist"
[<-,List-method Class "List"
[<-,Massvectorlist-method Class "Massvectorlist"
[[<-,List-method Class "List"
[[<-,Massvectorlist-method Class "Massvectorlist"
[[<-,Mlist-method Class "Mlist"