Package: cancerGI 1.0.1
cancerGI: Analyses of Cancer Gene Interaction
Functions to perform the following analyses: i) inferring epistasis from RNAi double knockdown data; ii) identifying gene pairs of multiple mutation patterns; iii) assessing association between gene pairs and survival; and iv) calculating the smallworldness of a graph (e.g., a gene interaction network). Data and analyses are described in Wang, X., Fu, A. Q., McNerney, M. and White, K. P. (2014). Widespread genetic epistasis among breast cancer genes. Nature Communications. 5 4828. <doi:10.1038/ncomms5828>.
Authors:
cancerGI_1.0.1.tar.gz
cancerGI_1.0.1.zip(r-4.5)cancerGI_1.0.1.zip(r-4.4)cancerGI_1.0.1.zip(r-4.3)
cancerGI_1.0.1.tgz(r-4.4-any)cancerGI_1.0.1.tgz(r-4.3-any)
cancerGI_1.0.1.tar.gz(r-4.5-noble)cancerGI_1.0.1.tar.gz(r-4.4-noble)
cancerGI_1.0.1.tgz(r-4.4-emscripten)cancerGI_1.0.1.tgz(r-4.3-emscripten)
cancerGI.pdf |cancerGI.html✨
cancerGI/json (API)
| # Install 'cancerGI' in R: |
| install.packages('cancerGI', repos = c('https://audreyqyfu.r-universe.dev', 'https://cloud.r-project.org')) |
- RNAi - Molecular phenotypes from single and double knockdowns in RNAi screen
- mutations - Genetic mutation data in patients.
- survival - Patient survival data.
- tested_pairs - Gene pairs tested in the double knockdown assay.
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 1 years agofrom:6ec6ae0c5b. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 22 2024 |
| R-4.5-win | OK | Nov 22 2024 |
| R-4.5-linux | OK | Nov 22 2024 |
| R-4.4-win | OK | Nov 22 2024 |
| R-4.4-mac | OK | Nov 22 2024 |
| R-4.3-win | OK | Nov 22 2024 |
| R-4.3-mac | OK | Nov 22 2024 |
Exports:computeSmallWorldnesscomputeSurvivalPValueForGenePairSet.outputcomputeSurvivalPValueGenePairAll.outputcomputeSurvivalPValueOneGenePaircomputeSurvivalPValueOneGenePair.outputconstructDesignMatrixprocessDataMutSurvtestMutationalPatternAll.wrapper
Dependencies:abindbackportsbootbroomcarcarDataclicolorspacecowplotcpp11DerivdoBydplyrfansifarverFormulagenericsggplot2gluegtableigraphisobandlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigplyrpurrrquantregqvalueR6RColorBrewerRcppRcppEigenreshape2rlangsandwichscalesSparseMstringistringrsurvivalsystemfittibbletidyrtidyselectutf8vctrsviridisLitewithrzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute smallworldness of a graph | computeSmallWorldness |
| Survival analysis for pairs of genes | computeSurvivalPValueForGenePairSet.output |
| Survival analysis for pairs of genes (with matched individuals) | computeSurvivalPValueGenePairAll.output |
| Survival analysis for one pair of genes | computeSurvivalPValueOneGenePair |
| Write results from survival analysis to output for one pair of genes | computeSurvivalPValueOneGenePair.output |
| Generate a design matrix from raw RNAi data. | constructDesignMatrix |
| Genetic mutation data in patients. | mutations |
| Find matched individuals in mutation and survival data | processDataMutSurv |
| Molecular phenotypes from single and double knockdowns in RNAi screen | RNAi |
| Patient survival data. | survival |
| Gene pairs tested in the double knockdown assay. | tested_pairs |
| Compute the p and q values of all pairwise gene mutation patterns | testMutationalPatternAll.wrapper |
