Calibration and filtering of mass spectrometric peak(mass) lists.


[Package List] [Top]

Documentation for package `mscalib' version 1.0.1

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

A C D G I M N P R S T W misc

-- A --

applycalib,Calibextstat,Massvector-method Class "Calibextstat"
applycalib,Calibintstat,Massvector-method Class "Calibintstat" : Internal calibration
applycalib,Calibintstat,Massvectorlist-method Class "Calibintstat" : Internal calibration
applycalib,Calibprestat,Massvector-method Class "Calibprestat": peptide rule based calibration
applycalib,Massvector,Calibextstat-method Class "Calibextstat"
applycalib,Massvector,Calibintstat-method Class "Calibintstat" : Internal calibration
applycalib,Massvector,Calibprestat-method Class "Calibprestat": peptide rule based calibration
applycalib,Massvector,Surf-method Class "Surf"
applycalib,Massvectorlist,Calibextstat-method Class "Calibextstat"
applycalib,Massvectorlist,Calibintlist-method Class "Calibintlist"
applycalib,Massvectorlist,Calibintstat-method Class "Calibintstat" : Internal calibration
applycalib,Massvectorlist,Calibprelist-method Class "Calibprelist" - peptide rule based calibration
applycalib,Massvectorlist,Calibprestat-method Class "Calibprestat": peptide rule based calibration
applycalib,Massvectorlist,Surf-method Class "Surf"
applycalib,Surf,Massvector-method Class "Surf"
applycalib,Surf,Massvectorlist-method Class "Surf"

-- C --

cal Tryptic autoproteolysis masses
cal2 Tryptic autoproteolysis masses
Calibextstat-class Class "Calibextstat"
Calibintlist-class Class "Calibintlist"
Calibintstat-class Class "Calibintstat" : Internal calibration
Caliblist-class Class "Caliblist"
Calibprelist-class Class "Calibprelist" - peptide rule based calibration
Calibprestat-class Class "Calibprestat": peptide rule based calibration
CalibPRstat-class Class "CalibPRstat" - Testing
Calibstat-class Class "Calibstat" - Generic calibration object class
coerce,Calibintlist,data.frame-method Class "Calibintlist"
coerce,Calibintstat,list-method Class "Calibintstat" : Internal calibration
coerce,Calibintstat,numeric-method Class "Calibintstat" : Internal calibration
coerce,Caliblist,data.frame-method Class "Caliblist"
coerce,Caliblist,matrix-method Class "Caliblist"
coerce,Calibprestat,list-method Class "Calibprestat": peptide rule based calibration
coerce,Calibprestat,numeric-method Class "Calibprestat": peptide rule based calibration
coerce,Calibstat,data.frame-method Class "Calibstat" - Generic calibration object class
coerce,Calibstat,list-method Class "Calibstat" - Generic calibration object class
coerce,Calibstat,numeric-method Class "Calibstat" - Generic calibration object class
coerce<-,Calibintlist,data.frame-method Class "Calibintlist"
coerce<-,Calibintstat,list-method Class "Calibintstat" : Internal calibration
correctinternal,Massvector,Massvector-method Corrects the masses using internal calibration
correctinternal,Massvectorlist,Massvector-method Corrects the masses using internal calibration
correctinternal-methods Corrects the masses using internal calibration
CSKrig-class Class "CSKrig"
CSsurf-class Class "CSsurf"
CSsurf.gls,Caliblist-method Spatial calibration model for sample support
CSsurf.gls-methods Spatial calibration model for sample support
CSsurf.ls,Caliblist-method Obtains calibration model for mass spectrometric support.
CSsurf.ls-methods Obtains calibration model for mass spectrometric support.
CSTps,Caliblist-method Thin plate spline from Caliblist
CSTps-methods Thin plate spline from Caliblist

-- D --

diffFilter,Massvector,Massvector-method Remove mass differences
diffFilter,Massvectorlist,Massvector-method Remove mass differences
diffFilter-methods Remove mass differences

-- G --

getdiff,Massvector-method Computes all mass differences in and massvectorlist.
getdiff,Massvectorlist-method Computes all mass differences in and massvectorlist.
getdiff-methods Computes all mass differences in and massvectorlist.
getextcalib,Massvector,Massvector-method Obtain external calibration model from poly-mer samples
getextcalib,Massvectorlist,Massvector-method Obtain external calibration model from poly-mer samples
getextcalib,Massvectorlist,missing-method Obtain external calibration model from poly-mer samples
getextcalib-methods Obtain external calibration model from poly-mer samples
getglobalcalib,Massvectorlist,Massvector-method Obtain calibration coefficients by internal global calibration
getglobalcalib,Massvectorlist,NULL-method Obtain calibration coefficients by internal global calibration
getglobalcalib-methods Obtain calibration coefficients by internal global calibration
getintcalib,Massvector,Massvector-method Obtain calibration coefficients using internal calibration
getintcalib,Massvectorlist,Massvector-method Obtain calibration coefficients using internal calibration
getintcalib-methods Obtain calibration coefficients using internal calibration
getLpepcalib,Massvectorlist-method Peptide role based calibration (preliminary) for aligned Massvectorlists
getLpepcalib-methods Peptide role based calibration (preliminary) for aligned Massvectorlists
getmstCalib,Massvectorlist-method ~~ Methods for Function getmstCalib in Package `mscalib' ~~
getmstCalib-methods ~~ Methods for Function getmstCalib in Package `mscalib' ~~
getpepcalib,Massvector-method Obtain calibration coefficients. (preliminary)
getpepcalib,Massvectorlist-method Obtain calibration coefficients. (preliminary)
getpepcalib,numeric-method Obtain calibration coefficients. (preliminary)
getpepcalib-methods Obtain calibration coefficients. (preliminary)
getPPGmasses Compute poly-(propylene glycol) masses
getPRcalib,Massvector-method ~~ Methods for Function getPRcalib in Package `mscalib' ~~
getPRcalib,Massvectorlist-method ~~ Methods for Function getPRcalib in Package `mscalib' ~~
getPRcalib-methods ~~ Methods for Function getPRcalib in Package `mscalib' ~~
getprecalib,Massvector-method Wool Smilansky peptide rule based calibration
getprecalib,Massvectorlist-method Wool Smilansky peptide rule based calibration
getprecalib,numeric-method Wool Smilansky peptide rule based calibration
getprecalib-methods Wool Smilansky peptide rule based calibration
globalcalib,Massvectorlist,Massvector-method Calibrate Massvectorlist by internal global calibration
globalcalib-methods Calibrate Massvectorlist by internal global calibration

-- I --

image,CSKrig-method Class "CSKrig"
image,CSsurf-method Class "CSsurf"

-- M --

massFilter,Massvector-method Methods for Function massFilter in Package `mscalib' (preliminary)
massFilter-methods Methods for Function massFilter in Package `mscalib' (preliminary)
mstCalib-class Class "mstCalib"

-- N --

NPPG Mass Spectra of protein and ppg samples

-- P --

pepFilter,Massvector-method Methods for Function pepFilter in Package `mscalib' (preliminary)
pepFilter,Massvectorlist-method Methods for Function pepFilter in Package `mscalib' (preliminary)
pepFilter-methods Methods for Function pepFilter in Package `mscalib' (preliminary)
peproleFilter,Massvector-method Methods for Function peproleFilter in Package `mscalib' (prliminary)
peproleFilter,Massvectorlist-method Methods for Function peproleFilter in Package `mscalib' (prliminary)
peproleFilter-methods Methods for Function peproleFilter in Package `mscalib' (prliminary)
plot,Calibextstat,missing-method Class "Calibextstat"
plot,Calibintstat,missing-method Class "Calibintstat" : Internal calibration
plot,Calibprestat,missing-method Class "Calibprestat": peptide rule based calibration
plot,CSKrig,missing-method Class "CSKrig"
plot,CSsurf,missing-method Class "CSsurf"

-- R --

residuals,ANY-method ~~ Methods for Function residuals in Package `mscalib' ~~
residuals,Massvector-method ~~ Methods for Function residuals in Package `mscalib' ~~
residuals,Massvectorlist-method ~~ Methods for Function residuals in Package `mscalib' ~~
residuals-methods ~~ Methods for Function residuals in Package `mscalib' ~~

-- S --

samples Mass Spectra of protein and ppg samples
show,Calibextstat-method Class "Calibextstat"
show,Calibintstat-method Class "Calibintstat" : Internal calibration
show,Caliblist-method Class "Caliblist"
show,Calibprestat-method Class "Calibprestat": peptide rule based calibration
show,Calibstat-method Class "Calibstat" - Generic calibration object class
summary,Caliblist-method Class "Caliblist"
summary,Calibstat-method Class "Calibstat" - Generic calibration object class
Surf-class Class "Surf"

-- T --

thebigcalib,mstCalib-method Class "mstCalib"

-- W --

wsFilter,Massvector-method Filtering of nonpeptide peaks
wsFilter,Massvectorlist-method Filtering of nonpeptide peaks
wsFilter-methods Filtering of nonpeptide peaks

-- misc --

[,Caliblist-method Class "Caliblist"
[[<-,Caliblist-method Class "Caliblist"