Massvector-class {msbase}R Documentation

Class "Massvector"

Description

A concise (1-5 lines) description of what the class is.

Objects from the Class

Objects can be created by calls of the form new("Massvector", data, info, tcoor, gelcoor, access, pionm).

Slots

.Data:
Object of class "matrix". First column contains masses. Second can contain intesnities.
info:
Object of class "character"
tcoor:
Object of class "numeric"
gelcoor:
Object of class "numeric"
access:
Object of class "character"
pionm:
Object of class "numeric"

Extends

Class "matrix", directly.

Methods

[
signature(x = "Massvector"): ...
coerce
signature(from = "Massvector", to = "array"): ...
coerce
signature(from = "Massvector", to = "list"): ...
coerce
signature(from = "Massvector", to = "data.frame"): ...
fintersect
signature(obx = "Massvector", oby = "Massvector"): ...
fis.element
signature(obx = "Massvector", oby = "Massvector"): ...
fmatch
signature(obx = "Massvector", oby = "Massvector"): ...
fmatchall
signature(obx = "Massvector", oby = "Massvector"): ...
fsetdiff
signature(obx = "Massvector", oby = "Massvector"): ...
fsetdiff
signature(obx = "Massvectorlist", oby = "Massvector"): ...
fsetequal
signature(obx = "Massvector", oby = "Massvector"): ...
funion
signature(obx = "Massvector", oby = "Massvector"): ...
gamasses
signature(object = "Massvector"): ...
image
signature(x = "Massvector"): ...
initialize
signature(.Object = "Massvector"): ...
length
signature(x = "Massvector"): ...
mvmeannorm
signature(object = "Massvector"): ...
mvscale
signature(object = "Massvector"): ...
nrmatch
signature(obx = "Massvector", oby = "Massvector"): ...
nrmatch
signature(obx = "Massvectorlist", oby = "Massvector"): ...
plot
signature(x = "Massvector", y = "Massvector"): ...
plot
signature(x = "Massvector", y = "missing"): ...
readBruker
signature(object = "Massvector"): reads Bruker XML file
readMV
signature(object = "Massvector", src = "character"): reads Massvector from file
show
signature(object = "Massvector"):
summary
signature(object = "Massvector"):
writeMV
signature(object = "Massvector", path = "character"): writes Massvector to file

Note

Author(s)

Witold E. Wolski witek96@users.sourceforge.net http://r4proteomics.sourceforge.net

See Also

fdist-methods,fbinary-methods,fcor-methods, or Massvectorlist-class

Examples

data(pldata)
new("Massvector")
new("Massvector",matrix(1:20,ncol=2),info="dummy",tcoor=c(0,0),gelcoor=c(0,0))
pl1<-pldata[[1]]
pl2<-pldata[[2]]
pl1
plot(pl1)
image(pl1)
length(pl1)
nrmatch(pl1,pl2,error=200,ppm=TRUE)
#returns indices of matching peaks.
fmatch(pl1,pl2,error=200,ppm=TRUE,uniq=TRUE)
#returns indices of matching and not matching peaks.
fmatchall(pl1,pl2,error=2,ppm=FALSE,uniq=TRUE)
funion(pl1,pl2,error=2,ppm=FALSE,uniq=TRUE)
fis.element(pl1,pl2,error=2,ppm=FALSE,uniq=TRUE)
fsetdiff(pl1,pl2,error=2,ppm=FALSE,uniq=TRUE)
fintersect(pl1,pl2,error=2,ppm=FALSE,uniq=TRUE)

[Package msbase version 1.0.0 Index]