Creating flow variables with R-Snippet works, but...

[andorak]

...not completely in the right way.

I am using an R-Snippet to read an external .txt file (parameter file). These parameters are then mapped to a list of flow variables. I want to send these to an OpenMS-node (MSGFPlusAdapter, node for protein identification) to use the parameters specified in the external .txt file instead of default or manually chosen values.

The flow variables are sucessfully created with:

parameters <- knime.in #receives parameter file from r source node
rownames(parameters) <- parameters[,1]
knime.out <- parameters

# write flow variables from parameter file
knime.flow.out <- list(	tolerance = as.double(parameters["tolerance",2]),
			chargeRange_min = parameters["chargeRange_min",2], 
			chargeRange_max = parameters["chargeRange_max",2],
			lengthRange_min = parameters["lengthRange_min",2],
			lengthRange_max = parameters["lengthRange_max",2],
			instrument = as.character(parameters["instrument",2]),
			enzyme = as.character(parameters["enzyme",2]),
			fragmentation = as.character(parameters["fragmentation",2]),
			protocol= as.numeric(parameters["protocol",2]),
			isotopeError_min = parameters["isotopeError_min",2], 
			isotopeError_max = parameters["isotopeError_max",2],
			matches = as.numeric(parameters["matches",2]),
			ntt = as.numeric(parameters["ntt",2]),
			tda = as.numeric(parameters["tda",2]),
			mods_count = as.numeric(1)
				)

 

Now, if I check the created variables internally in the R-Script everything looks fine:

http://imgur.com/a/Y6cLz #1

However if I check the Data output of the node and then the flow variables list it looks like this, the values are all wrong:

http://imgur.com/a/Y6cLz #2

Anybody knows a solution? Maybe I have to specify the data types in an other way in the script?

Thanks for your time and help!

[jonfuller]

Hi Andorak,

It looks like the two screenshots point to the same URL, so I can't quite see what the issue is. Could you update the screenshot links?

Thanks,

Jon

[andorak]

The Url provides a site with both screenshots titled #1 and #2.

You should be able to scroll down a bit and see it.

[jonathan.hale]

Hi andorak!

Your output in #1 shows that the values which are incorrect seem to be printed as factors (Hence the "n Levels" displayed after). As far as I understand these values should be numerical?

Can you please try wrapping `as.numeric()` around e.g. chargeRange_min/max?

...
chargeRange_min = as.numeric(parameters["chargeRange_min",2]),
...

I cannot try this, as I don't know what your `parameters` variable looks like...

Hope this helps!

Jonathan