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.

Install the latest version of this package by entering the following in R:
install.packages("snpRF")
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

View on CRAN

Functions

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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