integIRTy: Integrating Multiple Modalities of High Throughput Assays Using Item Response Theory
Version 1.0.0

This package provides a systematic framework for integrating multiple modalities of assays profiled on the same set of samples. The goal is to identify genes that are altered in cancer either marginally or consistently across different assays. The heterogeneity among different platforms and different samples are automatically adjusted so that the overall alteration magnitude can be accurately inferred.

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AuthorPan Tong, Kevin R Coombes
Date of publication2015-05-26 18:30:42
MaintainerPan Tong <nickytong@gmail.com>
LicenseApache License (== 2.0)
Version1.0.0
URL http://oompa.r-forge.r-project.org/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("integIRTy", repos="http://R-Forge.R-project.org")

Man pages

calculatePermutedScoreByGeneSampling: Calculate the permuted latent trait by gene sampling
computeAbility: Calculate latent traits for a given response matrix and item...
datasets: Ovarian Cancer Datasets
dichotomize: A wrapper that is able to dichotomize expression, methylation...
dichotomizeCN: Dichotomizing copy number data based on segmented data (i.e....
dichotomizeExpr: Dichotomize the expression data given both tumor and normal...
dichotomizeMethy: Dichotomize the methylation data given both tumor and normal...
fitOnSinglePlat: Fit IRT model on a single platform
intIRTeasyRun: The easyrun function for integrating multiple modalities of...
intIRTeasyRunFromRaw: The easyrun function for integrating multiple modalities of...
simulateBinaryResponseMat: Simulate binary response matrix according to 2-parameter Item...

Functions

CN_N Man page
CN_T Man page
Expr_N Man page
Expr_T Man page
Ii Source code
Methy_N Man page
Methy_T Man page
OV Man page
Pi Source code
Zscore2Binary Source code
bimodalIndex Source code
calculatePermutedScoreByGeneSampling Man page Source code
computeAbility Man page Source code
dichotomize Man page Source code
dichotomizeCN Man page Source code
dichotomizeExpr Man page Source code
dichotomizeMethy Man page Source code
fitOnSinglePlat Man page Source code
intIRTeasyRun Man page Source code
intIRTeasyRunFromRaw Man page Source code
simulateBinaryResponseMat Man page Source code
thetaEst Source code

Files

DESCRIPTION
NAMESPACE
R
R/Ii.R
R/Pi.R
R/calculatePermutedScoreByGeneSampling.R
R/computeAbility.R
R/fitOnSinglePlat.R
R/intIRTeasyRun.R
R/intIRTeasyRunFromRaw.R
R/miscellaneous.R
R/simulateBinaryResponseMat.R
R/thetaEst.R
build
build/vignette.rds
data
data/OV.rda
inst
inst/doc
inst/doc/integIRTy.R
inst/doc/integIRTy.Rnw
inst/doc/integIRTy.pdf
man
man/calculatePermutedScoreByGeneSampling.Rd
man/computeAbility.Rd
man/datasets.Rd
man/dichotomize.Rd
man/dichotomizeCN.Rd
man/dichotomizeExpr.Rd
man/dichotomizeMethy.Rd
man/fitOnSinglePlat.Rd
man/intIRTeasyRun.Rd
man/intIRTeasyRunFromRaw.Rd
man/simulateBinaryResponseMat.Rd
tests
tests/easytest.R
tests/easytest.Rout.save
tests/rawtest.R
tests/rawtest.Rout.save
vignettes
vignettes/integIRTy.Rnw
vignettes/integIRTy.bib
integIRTy documentation built on May 21, 2017, 3:48 a.m.