Package: integIRTy 1.0.9

Kevin R. Coombes

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

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. See Tong and Coombes (2012) <doi:10.1093/bioinformatics/bts561>.

Authors:Pan Tong [aut], Kevin R. Coombes [aut, cre]

integIRTy_1.0.9.tar.gz
integIRTy_1.0.9.zip(r-4.7-any)integIRTy_1.0.9.zip(r-4.6-any)
integIRTy_1.0.9.tar.gz(r-4.7-any)integIRTy_1.0.9.tar.gz(r-4.6-any)
integIRTy_1.0.9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
integIRTy/json (API)

# Install 'integIRTy' in R:

install.packages('integIRTy', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

CN_N - Ovarian Cancer Datasets
CN_T - Ovarian Cancer Datasets
Expr_N - Ovarian Cancer Datasets
Expr_T - Ovarian Cancer Datasets
Methy_N - Ovarian Cancer Datasets
Methy_T - Ovarian Cancer Datasets

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.43 score 27 scripts 344 downloads 10 exports 27 dependencies

Last updated from:1fc9f46b14. Checks:6 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	143
source / vignettes	OK	213
linux-release	OK	154
windows-devel	OK	92
windows-release	OK	90
wasm-release	OK	124

Exports:calculatePermutedScoreByGeneSampling computeAbility dichotomize dichotomizeCN dichotomizeExpr dichotomizeMethy fitOnSinglePlat intIRTeasyRun intIRTeasyRunFromRaw simulateBinaryResponseMat

Dependencies:abind admisc cli codetools doParallel expm foreach generics glue iterators lattice lifecycle ltm magrittr MASS Matrix mclust msm mvtnorm pillar pkgconfig polycor rlang survival tibble utf8 vctrs

integIRTy Vignette

Introduction | A Quick Example | Building The Pipeline Step By Step | Parallelizing integIRTy | File Location and Session Info

Rendered fromintegIRTy.Rnwusingutils::Sweave

Last update: 2017-07-11
Started: 2017-07-11

Help page	Topics
Calculate the permuted latent trait by gene sampling	calculatePermutedScoreByGeneSampling
Calculate latent traits for a given response matrix and item parameters using MLE	computeAbility
A wrapper that is able to dichotomize expression, methylation and CN data	dichotomize
Dichotomizing copy number data based on segmented data (i.e. log2ratio).	dichotomizeCN
Dichotomize the expression data given both tumor and normal samples.	dichotomizeExpr
Dichotomize the methylation data given both tumor and normal controls.	dichotomizeMethy
Fit IRT model on a single platform	fitOnSinglePlat
The easyrun function for integrating multiple modalities of high throughput assays using binary input matrix.	intIRTeasyRun
The easyrun function for integrating multiple modalities of high throughput assays using raw data.	intIRTeasyRunFromRaw
Ovarian Cancer Datasets	CN_N CN_T Expr_N Expr_T Methy_N Methy_T OV
Simulate binary response matrix according to 2-parameter Item Characteristic Function for given latent traits and item parameters.	simulateBinaryResponseMat

Package: integIRTy 1.0.9

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

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)