snpRF: 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.

Author
Fortran original by Leo Breiman and Adele Cutler, R port by Andy Liaw and Matthew Wiener. Modifications of randomForest v 4.6-7 for SNPs by Greg Jenkins based on a method developed by Stacey Winham, Greg Jenkins and Joanna Biernacka.
Date of publication
2015-01-20 18:41:24
Maintainer
Greg Jenkins <jenkins.gregory@mayo.edu>
License
GPL (>= 2)
Version
0.4

View on CRAN

Man pages

classCenter
Prototypes of groups.
combine
Combine Ensembles of Trees
getTree
Extract a single tree from a forest.
grow
Add trees to an ensemble
importance
Extract variable importance measure
margin
Margins of snpRF Classifier
MDSplot
Multi-dimensional Scaling Plot of Proximity matrix from snpRF
na.roughfix
Rough Imputation of Missing Values
outlier
Compute outlying measures
plot.snpRF
Plot method for snpRF objects
predict.snpRF
predict method for snpRF objects
snpRF
Classification with Random Forest for SNP Data
snpRFcv
Random Forest Cross-Valdidation for feature selection
snpRFexample
Simulated genetic data
snpRFImpute
Missing Value Imputations by snpRF
snpRFNews
Show the NEWS file
treesize
Size of trees in an ensemble
tuneSnpRF
Tune snpRF for the optimal mtry parameter
varImpPlot
Variable Importance Plot
varUsed
Variables used in a random forest

Files in this package

snpRF
snpRF/COPYING
snpRF/inst
snpRF/inst/CITATION
snpRF/inst/NEWS
snpRF/src
snpRF/src/rf.h
snpRF/src/regTree.c
snpRF/src/rf.c
snpRF/src/rfsub.f
snpRF/src/classTree.c
snpRF/src/regrf.c
snpRF/src/rfutils.c
snpRF/NAMESPACE
snpRF/data
snpRF/data/snpRFexample.rda
snpRF/R
snpRF/R/getTree.R
snpRF/R/combine.R
snpRF/R/varUsed.R
snpRF/R/snpRFNews.R
snpRF/R/MDSplot.R
snpRF/R/outlier.R
snpRF/R/snpRF.R
snpRF/R/grow.R
snpRF/R/print.snpRF.R
snpRF/R/tuneSnpRF.R
snpRF/R/na.roughfix.R
snpRF/R/snpRFcv.R
snpRF/R/treesize.R
snpRF/R/classCenter.R
snpRF/R/varImpPlot.R
snpRF/R/predict.snpRF.R
snpRF/R/margin.R
snpRF/R/snpRFImpute.R
snpRF/R/importance.R
snpRF/R/plot.snpRF.R
snpRF/R/zzz.R
snpRF/MD5
snpRF/DESCRIPTION
snpRF/man
snpRF/man/snpRFexample.Rd
snpRF/man/margin.Rd
snpRF/man/combine.Rd
snpRF/man/snpRFcv.Rd
snpRF/man/varUsed.Rd
snpRF/man/grow.Rd
snpRF/man/plot.snpRF.Rd
snpRF/man/snpRFImpute.Rd
snpRF/man/getTree.Rd
snpRF/man/predict.snpRF.Rd
snpRF/man/classCenter.Rd
snpRF/man/MDSplot.Rd
snpRF/man/outlier.Rd
snpRF/man/snpRFNews.Rd
snpRF/man/tuneSnpRF.Rd
snpRF/man/na.roughfix.Rd
snpRF/man/varImpPlot.Rd
snpRF/man/treesize.Rd
snpRF/man/importance.Rd
snpRF/man/snpRF.Rd