README.md
In jtleek/tspreg: Top scoring pairs regression

tspreg

An R package for performing top-scoring pairs regression. The basic idea is to look for pairs of genes that switch rankings between phenotypes. The tspreg package allows the discovery of top-scoring pairs for multi-class classification and for survival classification.

Installation

## If needed
install.packages("devtools")

## Install pre-requisite packages from Bioconductor
source("http://bioconductor.org/biocLite.R")
biocLite("genefilter")

source("http://bioconductor.org/biocLite.R")
biocLite("tspair")

## Install the survhd package from Bitbucket

install_bitbucket(repo="survhd",user="lwaldron",ref="default")

Use

library(tspair)
library(tspreg)
data(tspdata)

## Build a top-scoring pairs regression predictor

tspr1 <- tspreg(dat,as.factor(grp),npair=1)

# Shows the pairs of indices contributing to the predictor

tspr1$index

# Create the data frame for prediction

predictors <- calculateTspairs(dat,tspr1$index)

# Fit the linear model and predict

modelFit <- lm(grp=="diseased" ~ .,data=predictors$pairMat)


# Get the pairs on the test data set

validationPredictors <- calculateTspairs(dat2,tspr1$index)

# Apply predictor to test data set

predict(modelFit,newdata=validationPredictors$pairMat) > 0.5