TOMFlowPlot issue in autism demo
Closed this issue · 5 comments
I am just running through the Vignette with the demo data and I am having issues with this section
networks = c("autism", "controls") toms = lapply(networks, function(x) { load(paste0(x, '-block.1.RData')) get("TOM") })
It returns the error:
Warning: cannot open compressed file 'autism-block.1.RData', probable reason 'No such file or directory'Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
I already checked that saveTOMs = TRUE in the constructNetworks function. Any suggestions?
Hi @hannahthomas1235 ,
Did you check if it wrote that rds file during network construction? Maybe it called it something else for some reason?
I don't think that the rds files are being generated at all during network construction. I haven't changed any code, but I am running the latest R.
Okay, thank you for the info. Then there seems to be an issue with the constructNetwork function. Are you using saveTOMs = TRUE? Perhaps you don't have write permissions to the directory you're running the vignette in?
The vignette seems to be compiling properly on bioconductor: https://bioconductor.org/packages/3.20/bioc/vignettes/multiWGCNA/inst/doc/autism_full_workflow.html
I would also make sure you have the newest version of the package since that section of the vignette is recent. You can install from development as shown in the vignette.
Closing for now, but let me know if it's not resolved I can reopen.