I'm am a PhD student coming from a non-bio-informatics background dipping my toes in RRBS analysis using RnBeads.
I imported Bismarkcov files using the rnb.run.import function. I next wanted to save the RnBiseqSet object with the save.rnb.set function. I get the following error for (all) my files:
Error in ffsave(list = ls(ee), envir = ee, file = ffFn, ...) :
the previous files do not match the rootpath (case sensitive)
All mentioned files are of the format .ff and are located in the directory ~/Rtmp2BkJtI/ff
When I look at the save.rnb.set code, I see that it uses getOption('fftempdir') as argument for rootpath:
When I simply run getOption('fftempdir'), I get exactly the same directory as the one my files are in:
Any suggestions how to remedy this issue?