snpRF: Random Forest for SNPs to Prevent X-chromosome SNP Importance Bias
Version 0.4

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.

Browse man pages Browse package API and functions Browse package files

AuthorFortran 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 publication2015-01-20 18:41:24
MaintainerGreg Jenkins <jenkins.gregory@mayo.edu>
LicenseGPL (>= 2)
Version0.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("snpRF")

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

Functions

MDSplot Man page Source code
autosome.snps Man page
classCenter Man page Source code
combine Man page Source code
covariates Man page
gender Man page
getTree Man page Source code
grow Man page Source code
grow.default Man page Source code
grow.snpRF Man page Source code
importance Man page Source code
importance.default Man page Source code
importance.snpRF Man page Source code
margin Man page Source code
margin.default Man page Source code
margin.snpRF Man page Source code
mylevels Source code
na.roughfix Man page Source code
na.roughfix.data.frame Man page Source code
na.roughfix.default Man page Source code
onAttach Source code
outlier Man page Source code
outlier.default Man page Source code
outlier.snpRF Man page Source code
phenotype Man page
plot.margin Man page Source code
plot.snpRF Man page Source code
predict.snpRF Man page
print.snpRF Man page
snpRF Man page Source code
snpRFImpute Man page Source code
snpRFNews Man page Source code
snpRFcv Man page Source code
snpRFexample Man page
treesize Man page Source code
tuneSnpRF Man page Source code
varImpPlot Man page Source code
varUsed Man page Source code
xchrom.snps Man page
xchrom.snps.names Man page

Files

COPYING
inst
inst/CITATION
inst/NEWS
src
src/rf.h
src/regTree.c
src/rf.c
src/rfsub.f
src/classTree.c
src/regrf.c
src/rfutils.c
NAMESPACE
data
data/snpRFexample.rda
R
R/getTree.R
R/combine.R
R/varUsed.R
R/snpRFNews.R
R/MDSplot.R
R/outlier.R
R/snpRF.R
R/grow.R
R/print.snpRF.R
R/tuneSnpRF.R
R/na.roughfix.R
R/snpRFcv.R
R/treesize.R
R/classCenter.R
R/varImpPlot.R
R/predict.snpRF.R
R/margin.R
R/snpRFImpute.R
R/importance.R
R/plot.snpRF.R
R/zzz.R
MD5
DESCRIPTION
man
man/snpRFexample.Rd
man/margin.Rd
man/combine.Rd
man/snpRFcv.Rd
man/varUsed.Rd
man/grow.Rd
man/plot.snpRF.Rd
man/snpRFImpute.Rd
man/getTree.Rd
man/predict.snpRF.Rd
man/classCenter.Rd
man/MDSplot.Rd
man/outlier.Rd
man/snpRFNews.Rd
man/tuneSnpRF.Rd
man/na.roughfix.Rd
man/varImpPlot.Rd
man/treesize.Rd
man/importance.Rd
man/snpRF.Rd
snpRF documentation built on May 19, 2017, 6:51 p.m.