pickledgrape
commented
3 months ago On the reference data set I had this error after loading without doing any normalization or modification of imported data: Error in riskSignature(expr_input = normalized_expression, background = T) : unused argument (background = T)
This is an error in the vignette's suggested usage; indeed, "background" is not called in riskSignature(), but "use_background" is. Updating readME.
Successfully downloaded and tested on mFORGE and ran on unnormalized and log2(TPM+1) normalized RNAseq data
On the reference data set I had this error after loading without doing any normalization or modification of imported data:
Error in riskSignature(expr_input = normalized_expression, background = T) : unused argument (background = T)The documentation states that:background - Table consisting of a "universe" of genes analyzed during model training. I think this should just subsetexpr_inputbut the exact functionality should be better defined and also did not run in my test. I had to remove the variable to run.A test/return specific to exact data format needed would be useful. The current error return is:
Error in FUN(X[[i]], ...) : only defined on a data frame with all numeric-alike variableswhich is descriptive on its own, but a custom one can tell the user the exact format of the data required.I recommend adding more documentation to the RiskSignature function. Format can be based on another R package you think is high quality.
Maybe create an option in the function to export as CSV or some other data format when run. Could save users a small amount of time. If ambitious could also create/output some summary data, but is not necessary.