Class "MapCollection"

Description

This class holds several MareyMap-class objects organised by species (using SpeciesMaps-class object).

Objects from the Class

Objects can be created by calls of the form new("MapCollection", ...) or using the function MapCollection. You may as well use the default collection provided by the package (as data(mareymaps)).

Slots

species:

Object of class "list" containing a SpeciesMaps-class for each species of the collection.

Methods

[

signature(x = "MapCollection"): ...

[[<-

signature(x = "MapCollection", i = "ANY", j = "ANY", value = "SpeciesMaps"): ...

[[<-

signature(x = "MapCollection", i = "ANY", j = "ANY", value = "MareyMap"): ...

[[

signature(x = "MapCollection"): obtain the SpeciesMaps corresponding to a species name

$

signature(x = "MapCollection"): subset by species name

+

signature(e1 = "MapCollection", e2 = "MareyMap"): adds a map to the collection

+

signature(e1 = "MapCollection", e2 = "SpeciesMaps"): adds a species t the collection

coerce

signature(from = "MapCollection", to = "data.frame"): --> as(object,"data.frame")

speociesNames

signature(object = "MapCollection"): returns the list of the names of all species present in the collection

Author(s)

Clement Rezvoy <rezvoy@biomserv.univ-lyon1.fr>

See Also

SpeciesMaps-class MareyMap-class

Examples

data(mareymaps)
speciesNames(mareymaps)
human <- mareymaps[["Homo sapiens (deCODE)"]]
chr1 <- mareymaps[["Homo sapiens (deCODE)","Chromosome 01"]]
# do some useful changes to the map...
mapName(chr1)<- "Chrom 1 (modified)"
mareymaps <- mareymaps + chr1