Rfast::Rowsort
faeneeR opened this issue · 8 comments
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.
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?
My Rfast version is 1.8.5. But it seems that it doesn't contain the rowSort function.
Then update your Rfast! we have 2.0.7 version and now it will be realesed the 2.0.8
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 iaconogi/bigSCale2#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.
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.
Thanks for your generous help!
It would be so nice if you could tell me how to edit the file. Thanks a lot!
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.
Thanks a lot!!!