Class "databel"

databel-class {DatABEL} R Documentation

Class "databel"

Description

A class interfacing FILEVECTOR C++ library class FilteredMatrix for storage of and fast consecutive access to large data matrices in out-of-RAM disk mode with regulated cache size. Columns of matrix are accessible very quickly.

Objects from the Class

Objects can be created by calls of the form new("databel", baseobject) or databel(baseobject). FILEVECTOR data are stored using files of form BASE.fvi (index) and BASE.fvd (data). "baseobject" is either the BASE name, or object of class "databel".

Slots

usedRowIndex:
Object of class "integer" which rows are used
usedColIndex:
Object of class "integer" which columns are used
uninames:
Object of class "list", containing obejcts 'unique.names' – TRUE if all dimnames are unique; 'unique.colnames' – if column names are unique; 'unique.rownames' – if row names are unique
backingfilename:
Object of class "character" providing BASE name
cachesizeMb:
Object of class "integer" size of cache to be used to access the data. If cache is equal to the data size, the object is stored in RAM
data:
Object of class "externalptr", pointer to FilteredMatrix C++ object

Methods

[
signature(x = "databel"): sub-setting object
[<-
signature(x = "databel"): setting the values in the object
connect
signature(object = "databel"): connects the data files to R object (calls constructor of FilteredMatrix object, selects rows and columns)
disconnect
signature(object = "databel"): disconnects the data files to R object (calls destructor of FilteredMatrix object, selects rows and columns)
dim
signature(x = "databel"): returns dimensions of the matrix
dimnames
signature(x = "databel"): returns row and column names
dimnames<-
signature(x = "databel"): sets row and column names
set_dimnames<-
signature(x = "databel"): sets row and column names (these could be non-unique)
length
signature(x = "databel"): returns number of elements in the matrix
save_as
signature(x = "databel"): saves (a sub-set of) the object as FV-file
save_as_text
signature(x = "databel"): saves (a sub-set of) the object as plain text file
backingfilename
signature(object = "databel"): returns BASE FILEVECTOR file name used to store the data
cachesizeMb
signature(object = "databel"): returns the cache size used
cachesizeMb<-
signature(x = "databel"): sets new cache size
get_dimnames
signature(object = "databel"): returns the names of rows and columns, which may be non-unique
set_dimnames<-
signature(x = "databel"): set row and column names, which may be non-unique
setReadOnly<-
signature(x = "databel"): sets ReadOnly (TRUE or FALSE) attribute to 'databel' object

Author(s)

Yurii Aulchenko, Stepan Yakovenko, Andrey Chernyh

References

http://mga.bionet.nsc.ru/~yurii/ABEL/

See Also

make_empty_fvf, databel, matrix2databel

Examples

showClass("databel")

[Package DatABEL version 0.9-2 Index]