snpRF v0.4
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Random Forest for SNPs to Prevent X-chromosome SNP Importance Bias
A modification of Breiman and Cutler's classification random forests modified for SNP (Single Nucleotide Polymorphism) data (based on randomForest v4.6-7) to prevent X-chromosome SNP variable importance bias compared to autosomal SNPs by simulating the process of X chromosome inactivation. Classification is based on a forest of trees using random subsets of SNPs and other variables as inputs.
Functions in snpRF
| Name | Description | |
| tuneSnpRF | Tune snpRF for the optimal mtry parameter | |
| predict.snpRF | predict method for snpRF objects | |
| MDSplot | Multi-dimensional Scaling Plot of Proximity matrix from snpRF | |
| plot.snpRF | Plot method for snpRF objects | |
| na.roughfix | Rough Imputation of Missing Values | |
| snpRFNews | Show the NEWS file | |
| getTree | Extract a single tree from a forest. | |
| snpRFexample | Simulated genetic data | |
| varUsed | Variables used in a random forest | |
| varImpPlot | Variable Importance Plot | |
| combine | Combine Ensembles of Trees | |
| importance | Extract variable importance measure | |
| snpRFImpute | Missing Value Imputations by snpRF | |
| grow | Add trees to an ensemble | |
| margin | Margins of snpRF Classifier | |
| treesize | Size of trees in an ensemble | |
| snpRF | Classification with Random Forest for SNP Data | |
| outlier | Compute outlying measures | |
| classCenter | Prototypes of groups. | |
| snpRFcv | Random Forest Cross-Valdidation for feature selection | |
| No Results! | ||
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Details
| Date | 2014-01-20 |
| License | GPL (>= 2) |
| Packaged | 2015-01-20 14:16:23 UTC; jenkins |
| NeedsCompilation | yes |
| Repository | CRAN |
| Date/Publication | 2015-01-20 18:41:24 |
| depends | base (>= 2.5.0) , R (>= 2.5.0) , stats |
| suggests | MASS , RColorBrewer |
| Contributors | Fortran by Leo Breiman, Adele Cutler, R by Andy Liaw, Matthew Modifications of randomForest v |
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[](http://www.rdocumentation.org/packages/snpRF)