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snpRF (version 0.4)

Random Forest for SNPs to Prevent X-chromosome SNP Importance Bias

Description

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.

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Version

Install

install.packages('snpRF')

Monthly Downloads

8

Version

0.4

License

GPL (>= 2)

Maintainer

Greg Jenkins

Last Published

January 20th, 2015

Functions in snpRF (0.4)

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