add path to geneset for MCPCOUNTER

[anabbi]

Hello,

Just a note that the deconvolute function for MCPCOUNTER returns an error in cases where there is no internet access (eg, some institutional setups for compute nodes). This is because by default it tries to download the geneset from:

https://raw.githubusercontent.com/ebecht/MCPcounter/master/Signatures/genes.txt

It would be great if you can include the argument genes from MCPcounter.estimate that allows user to define the path to geneset.

Thanks

[grst]

Hi @anabbi,

thanks for reporting!
In fact, we could consider providing those files as part of the immunedeconv package. The MCP counter license should permit that.

[RichardCorbett]

Hi folks,
I just ran in to the exact same error. Someone is testing my code on a server without an internet connection and got the following error

>>> Running mcp_counter
Error in open.connection(file, "rt") :
  Timeout was reached: [raw.githubusercontent.com] Failed to connect to raw.githubusercontent.com port 80: Connection timed out
Calls: deconvolute ... <Anonymous> -> read.table -> open -> open.connection
Execution halted

I did some googling, found the genes.txt file listed above and came here to ask how it may be passed in to mcp_counter. @anabbi seems to have beat me to it by just a week!