createES function is not found in the package.

[uhatikus]

For some reason, createES function is not found in the package phantasus.

Example of behavior with the error: https://rdrr.io/bioc/phantasus/man/createES.html

Error:

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading config from /usr/lib/R/site-library/opencpu/config/defaults.conf
Error in createES(data, pData, varLabels, fData, fvarLabels, eData) : 
  could not find function "createES"
Execution halted

I have experienced the same behavior when I used phantasus locally:

[assaron]

Hi,

Could you please provide more context on how did you get the first error? createES is an internal function and is not exported, so that the behavior on the last screenshot is expected, it's available only as phantasus:::createES. However, it should not prevent it to be called within the Phantasus application, which apparently happens when you get the first error.

[uhatikus]

I have run the example on https://rdrr.io/bioc/phantasus/man/createES.html:

[assaron]

Ah, I see. createES is internal function and the corresponding documentation and examples are only for internal usage and aren't supposed to be run manually. Actually we need to add "internal" tag for this, so not to confuse users.

Anyway, if you want to open specifically prepared dataset from R you can prepare it as an ExpressionSet object and either save it to a GCT file with write.gct function and load it from the web-interface, or save it to and rda format and put it to the preloaded folder as described at https://ctlab.github.io/phantasus-doc/installation.html#preloaded-datasets

[uhatikus]

@assaron Thanks a lot! I will use the guide you sent me!

Lasttly, I would like to mention that createES also exists in pdf manual: https://www.bioconductor.org/packages/devel/bioc/manuals/phantasus/man/phantasus.pdf (maybe here it is also mentioned for internal usage)