Whenever I try to use eXstasy I get this error, probably due to a wrong argument passing to randomForest package:
$ ./extasy.rb -i 148.vcf -g geneprios/res/HP_0008872_fgs.tsv,geneprios/res/HP_0001249_fgs.tsv,geneprios/res/HP_0004322_fgs.tsv,geneprios/res/HP_0001999_fgs.tsv -c
2014-05-31 15:08:01 +0200: Sorting input VCF...
2014-05-31 15:08:01 +0200: Input VCF sorted...
2014-05-31 15:08:01 +0200: Finding missense mutations...
2014-05-31 15:08:35 +0200: Fetching features for variants...
2014-05-31 15:08:36 +0200: 50 missense variants annotated...
2014-05-31 15:08:36 +0200: Prioritizing against geneprios/res/HP_0008872_fgs.tsv
2014-05-31 15:08:36 +0200: Appending gene prioritization data...
2014-05-31 15:08:37 +0200: Data ready for eXtasy...
2014-05-31 15:08:37 +0200: Running eXtasy...
randomForest 4.6-7
Type rfNews() to see new features/changes/bug fixes.
Error in predict.randomForest(rf, d, type = "prob") :
New factor levels not present in the training data
Calls: predict -> predict.randomForest
Execution halted
This is my R configuration
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RobustRankAggreg_1.1 randomForest_4.6-7
loaded via a namespace (and not attached):
[1] tcltk_3.1.0 tools_3.1.0
Whenever I try to use eXstasy I get this error, probably due to a wrong argument passing to randomForest package:
This is my R configuration