[mamba-help] getpredictors.py

[Szabolcs S. <ssz...@tg...>]

Hi,
I am completely new to MAMBA and trying to figure out how you make NMD prediction work.

Reading  getpredictors.py script, I find that the 4th argument is the the input file for which NMD should be predicted.

Could you explain how you generate the input for this script? What is includes and in what format.
This is all I find in the script


## Variants to predict NMD
## Format: chr:pos ref alt af lofflag trnscaffected

Is this input file tab delimited or space?
is the lofflag  numerical  (0,1,2) or a character string (ie. nonsense, splice-site)
is trnscaffected numerical  (0,1,2) or a charctare string (ie. FULL, PARTIAL)

In addition, once the output file is created, would it become the input to the R predition script as newdata= ?

predict(modelFit.RF,newdata=tmp.data,type="prob",na.action=na.roughfix)


Thanks for your input,
Szabi

Szabolcs Szelinger
Research Associate
Neurogenomics Division, The Translational Genomics Research Institute (TGen)
445 N. 5th Street, Phoenix AZ 85044
ph:602-343-8723
ssz...@tg...<mailto:ssz...@tg...>



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