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I want to save a sparse and very large dgcMatrix onto disc. I read that it could be done with writeMM method. So, when I am trying to do that:

writeMM(UMI_count, "/home/gene_count_filtered/filtered_dataset")

Rstudio is giving me an error:

Error in writeMM(UMI_count, "/home/gene_count_filtered/filtered_dataset") : 
could not find function "writeMM"

Ok, I read that this function is in the Matrix package. I installed it, but when I try loading it:

library(Matrix)

I am getting another error due to other libraries using Matrix already on the lower level, as I understand:

Error in value[[3L]](cond) : 
Package ‘Matrix’ version 1.2.11 cannot be unloaded:
Error in unloadNamespace(package) : namespace ‘Matrix’ is imported by 
‘scran’, ‘scater’, ‘SummarizedExperiment’ so cannot be unloaded

I also tried justwrite.matrix(UMI_count, "/home/nikita/filtered_dataset"), but got an error:

Cholmod error 'out of memory' at file ../Core/cholmod_memory.c, line 147

What could be the solution to the problem? I just need to somehow save a very large dgcMatrix on disc.

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  • $\begingroup$ Which commands did you use to install Matrix? Did you use a fresh (with no environment) session? $\endgroup$
    – llrs
    Dec 20 '17 at 22:13
  • $\begingroup$ Nope, but I am having this object and I need to save it. I do not want to restart 10h calculation $\endgroup$ Dec 20 '17 at 22:43
  • $\begingroup$ you can install the package in a new instance of R $\endgroup$
    – llrs
    Dec 21 '17 at 0:05
  • $\begingroup$ But how am I going to save the matrix of the current session? That is the issue $\endgroup$ Dec 21 '17 at 0:17
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    $\begingroup$ Restarting R should fix this. There’s probably no way around this (you could try to manually unload all namespaces that use the Matrix package). $\endgroup$ Dec 21 '17 at 14:26
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Ultimately I just restarted Rstudio as Konrad Rudolph suggested, imported Matrix library, and then writeMM method worked just fine. However, rownames were converted into just numbers, but I needed to keep the gene names instead as it was in dgcMatrix, so after some search I found a different way of doing that from here:

http://www.sthda.com/english/wiki/saving-data-into-r-data-format-rds-and-rdata

So, I just did save() (and then, to load back - load()) and the rownames are maintained like I wanted it to be. So, storing it now as .RData file.

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