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
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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

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