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iaconogi / bigSCale2

Framework for clustering, phenotyping, pseudotiming and inferring gene regulatory networks from single cell data
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rowSort' is not an exported object from 'namespace:Rfast #37

Open faeneeR opened 1 year ago

faeneeR commented 1 year ago

when I try the Gene Regulatory Networks tutorial , the first step "results.ctl=compute.network(expr.data = expr.ctl,gene.names = gene.names)" reported an error: Error: 'rowSort' is not an exported object from 'namespace:Rfast'

faeneeR commented 1 year ago

and my package.version("Rfast") is "1.8.5"

atomadam2 commented 4 months ago

For anyone else who comes across this, there is now a pull request to fix this error caused by a change in Rfast.

If you want to fix it, and preserve a copy of this program you can download the whole repository, edit the line, and install that version in R.

On the Command Line, run git clone https://github.com/iaconogi/bigSCale2

This will download a local version of bigSCale2

Find the package in, for example C:\Users\XXX\bigSCale2\R

Open Functions.R

Make the following Change: Change line 3928 from: B=Rfast::rowVars(expr.row.sorted[,(num.samples-skwed.cells):num.samples], suma = NULL, std = TRUE)/a

To this (removing 'suma = NULL') B=Rfast::rowVars(expr.row.sorted[,(num.samples-skwed.cells):num.samples], std = TRUE)/a

Then in R, install this new version devtools::install('C:/Users/XXX/bigSCale2/')