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

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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.

Author
Pan Tong, Kevin R Coombes
Date of publication
2015-05-26 18:30:42
Maintainer
Pan Tong <nickytong@gmail.com>
License
Apache License (== 2.0)
Version
1.0.0
URLs

View on R-Forge

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...

Files in this package

integIRTy/DESCRIPTION
integIRTy/NAMESPACE
integIRTy/R
integIRTy/R/Ii.R
integIRTy/R/Pi.R
integIRTy/R/calculatePermutedScoreByGeneSampling.R
integIRTy/R/computeAbility.R
integIRTy/R/fitOnSinglePlat.R
integIRTy/R/intIRTeasyRun.R
integIRTy/R/intIRTeasyRunFromRaw.R
integIRTy/R/miscellaneous.R
integIRTy/R/simulateBinaryResponseMat.R
integIRTy/R/thetaEst.R
integIRTy/build
integIRTy/build/vignette.rds
integIRTy/data
integIRTy/data/OV.rda
integIRTy/inst
integIRTy/inst/doc
integIRTy/inst/doc/integIRTy.R
integIRTy/inst/doc/integIRTy.Rnw
integIRTy/inst/doc/integIRTy.pdf
integIRTy/man
integIRTy/man/calculatePermutedScoreByGeneSampling.Rd
integIRTy/man/computeAbility.Rd
integIRTy/man/datasets.Rd
integIRTy/man/dichotomize.Rd
integIRTy/man/dichotomizeCN.Rd
integIRTy/man/dichotomizeExpr.Rd
integIRTy/man/dichotomizeMethy.Rd
integIRTy/man/fitOnSinglePlat.Rd
integIRTy/man/intIRTeasyRun.Rd
integIRTy/man/intIRTeasyRunFromRaw.Rd
integIRTy/man/simulateBinaryResponseMat.Rd
integIRTy/tests
integIRTy/tests/easytest.R
integIRTy/tests/easytest.Rout.save
integIRTy/tests/rawtest.R
integIRTy/tests/rawtest.Rout.save
integIRTy/vignettes
integIRTy/vignettes/integIRTy.Rnw
integIRTy/vignettes/integIRTy.bib