I was asked privately
> I have been using <the Matrix package> extensively to
> calculate the relatedness-matrix based on the pedigree for
> our ornamental plants. I was wondering if you could give
> me some advice, for which I would like to thank you in
> advance!
> The output of the relatedness matrix I get from
> the nadiv package is a dsCMatrix. I would like to save it
> in some way, so I could query a subset of this matrix
> later on, as in most cases, the full matrix is not
> needed. Do you know what kind of format is ideal for
> data-storage (either in file or in a database) for a
> sparse matrix? Thanks in advance!
as that is a relative general question, I allow myself to answer
in public such that the answer my help others as well.
Let's use an example from package 'nadiv':
require(nadiv)
?makeA # to learn about the function
## create a largish example
Awarcol <- makeA(ggTutorial[1:2000, 1:3])
str(Awarcol)
nnzero(Awarcol)
object.size(Awarcol)
object.size(as.matrix(Awarcol)) # ~ 14 times large
image(Awarcol) # wait a bit .. ... but it's worth it!
-------------
> Awarcol <- makeA(ggTutorial[1:2000, 1:3])
> str(Awarcol)
Formal class 'dsCMatrix' [package "Matrix"] with 7 slots
..@ i : int [1:164107] 0 1 2 3 4 5 6 7 8 9 ...
..@ p : int [1:2001] 0 1 2 3 4 5 6 7 8 9 ...
..@ Dim : int [1:2] 2000 2000
..@ Dimnames:List of 2
.. ..$ : chr [1:2000] "1" "2" "3" "4" ...
.. ..$ : chr [1:2000] "1" "2" "3" "4" ...
..@ x : num [1:164107] 1 1 1 1 1 1 1 1 1 1 ...
..@ uplo : chr "U"
..@ factors : list()
> nnzero(Awarcol)
[1] 326214
> object.size(Awarcol)
2235112 bytes
> object.size(as.matrix(Awarcol))
32256488 bytes
>
------------------------------------------------
Now, save it (as file to current working directory) via
saveRDS(Awarcol, file = "makeA_warc.rds")
## and that is *only* 110 Kbytes :
> file.size("makeA_warc.rds")
[1] 115288
Or restore it in a later R session
Amat.warcol <- readRDS("makeA_warc.rds")
> str(Awarc)
Loading required package: Matrix
Formal class 'dsCMatrix' [package "Matrix"] with 7 slots
..@ i : int [1:164107] 0 1 2 3 4 5 6 7 8 9 ...
..@ p : int [1:2001] 0 1 2 3 4 5 6 7 8 9 ...
..@ Dim : int [1:2] 2000 2000
..@ Dimnames:List of 2
.. ..$ : chr [1:2000] "1" "2" "3" "4" ...
.. ..$ : chr [1:2000] "1" "2" "3" "4" ...
..@ x : num [1:164107] 1 1 1 1 1 1 1 1 1 1 ...
..@ uplo : chr "U"
..@ factors : list()
> image(Awarc)
>
Note how 'str(..)' automatically loaded the Matrix package
which you do need for image(<dsCMatrix>) to work nicely.
Best regards,
Martin
--
Martin Maechler
ETH Zurich and R Core team
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