Faster summarize by gene

[hfuchs5]

What changes are proposed in this pull request? Avoid use of pivot_*() functions in this because it was taking too long. I used base R matrices instead. Now it takes 10 seconds to run according to tictoc package.

If there is an GitHub issue associated with this pull request, please provide link.

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[michaelcurry1123]

in summarize_by_gene() on line 35 when you name the columns it is possible that they have the same name. After this you cannot use mutate or other dplyr functions. If you are trying to name the columns after the sample_id you can maybe do something like this: all_bin2[rownames(all_bin2)== "sample_id",]

[karissawhiting]

@hfuchs5 I made some updates to simplify how to handle sample_id (you're right that rownames can't be avoided unfortunately!) and add a few speed enhancements (e.g. using table() instead of summarise). I also added a check for numeric columns up front instead of transforming later which seems to speed things even more!

        test replications                elapsed            relative   user.self   sys.self
1      summarize_by_gene_new           500 161.339     1.000   156.353      5.092
2      summarize_by_gene               500 229.061    1.420   222.734      6.407

Could you test it out with your large data set to make sure it still is faster?

Thanks for your work on this. I think we are close!

[hfuchs5]

It ran through my dataset with 1000+ samples in 1.14 seconds! It looks good to me and I'm going to merge.