Introduction to Bioconductor in R
James Chapman
Curriculum Manager, DataCamp
Positive
plot()
and methods(plot)
Negative
Positive
Example: myDescriptor <- new("GenomeDescription")
Negative
Ask if an object is S4
isS4(myDescriptor)
TRUE
str
of S4 objects start with Formal class
str(myDescriptor)
Formal class 'GenomeDescription' [package "GenomeInfoDb"] with 7 slots
...
A class describes a representation
MyEpicProject <- setClass(# Define class name with UpperCamelCase
"MyEpicProject",
# Define slots, helpful for validation
slots = c(ini = "Date",
end = "Date",
milestone = "character"),
# Define inheritance
contains = "MyProject")
.S4methods(class = "GenomeDescription")
[1] coerce commonName organism provider
[5] providerVersion releaseDate releaseName seqinfo
[9] seqnames show toString bsgenomeName
see '?methods' for accessing help and source code
showMethods(classes = "GenomeDescription", where = search())
Object summary
show(myDescriptor)
| organism: ()
| provider:
| provider version:
| release date:
| release name:
| ---
| seqlengths:
Introduction to Bioconductor in R