Rfast::Rowsort

[faeneeR]

I'd like to ask whether you could provide a Rfast version that contain the Rowsort function because this function is needed when infering the putative gene regulatory network (GRN) in the bigScale2 package. AND here is the error:

results.ctl=compute.network(expr.data = expr.ctl,gene.names = gene.names) [1] "Pre-processing) Removing null rows " [1] "Discarding 4182 genes with all zero values" [1] "PASSAGE 1) Setting the size factors ...." [1] "PASSAGE 2) Setting the bins for the expression data ...." [1] "Creating edges..." [1] "47.2 % of elements < 10 counts, therefore Using a reads compatible binning" [1] "PASSAGE 3) Storing in the single cell object the Normalized data ...." [1] "PASSAGE 4) Computing the numerical model (can take from a few minutes to 30 mins) ...." [1] 22089 1313 [1] "I remove 1349 genes not expressed enough" [1] "Calculating normalized-transformed matrix ..." [1] "Computing transformed matrix ..." [1] "Converting sparse to full Matrix ..." [1] "Normalizing expression gene by gene ..." [1] "Calculating Pearson correlations ..." [1] "Clustering ..." [1] "Calculating optimal cut of dendrogram for pre-clustering" [1] "We are here" [1] "Pre-clustering: cutting the tree at 6.00 %: 15 pre-clusters of median(mean) size 84 (87.5333)" [1] "Computed Numerical Model. Enumerated a total of 1.11135e+09 cases"
[1] "PASSAGE 5) Clustering ..." [1] "Clustering cells down to groups of approximately 50-250 cells"

Recursive clustering, beginning round 1 ....[1] "Analyzing 1313 cells for ODgenes, min_ODscore=2.00" Error: 'rowSort' is not an exported object from 'namespace:Rfast'

And I have no where to find the Rfast version containing Rowsort function in CRAN. So I wonder if you could offer the loading url.

[ManosPapadakis95]

We do have a rowSort for numerical matrices in Rfast. I don't know what you mean by "providing a version". What version of Rfast do you have?

[faeneeR]

My Rfast version is 1.8.5. But it seems that it doesn't contain the rowSort function.

[ManosPapadakis95]

Then update your Rfast! we have 2.0.7 version and now it will be realesed the 2.0.8

[faeneeR]

Thanks for your work.

But it confused me that when I run the function compute.network() in bigSCale2 package, this process needs the Rfast::rowVars. So I have to downgrade the Rfast package back to earlier versions. Details can be seen in https://github.com/iaconogi/bigSCale2/issues/36.

So I changed my Rfast version into 1.8.5.

But later, I met another error when running the function compute.network() in bigSCale2 package. It is "Error: 'rowSort' is not an exported object from 'namespace:Rfast'".

Now I am so confused.

[ManosPapadakis95]

The problem is not that there isn't any rowSort function, but the usage of the depricated argument. This is not our fault. I have fix the issue and submit a change to bigScale2 package. You have to wait until the maintainer accept it. Although, you can just edit the file by your self and run the function.

[faeneeR]

Thanks for your generous help!

It would be so nice if you could tell me how to edit the file. Thanks a lot!

[ManosPapadakis95]

Just take the code of compute.network, search where the suma = NULL is, remove it and run the code in R. If you don't understand what I say it is better to wiati until the maintainers accept my pull request.

[faeneeR]

Thanks a lot!!!

[xiaoli-0709]

Thanks a lot!!!

I met the same problem again! I try to delete the code( suma = NULL ) in Functions.R at line 3928 and intall the packages again .But it still exits. Do you have any suggestions?