# Basic classes and methods for mass spectrometric mass list manipulation.

## Documentation for package `msbase' version 1.1.1

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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 --

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

## -- 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"