Package: ICSKAT 0.2.0
ICSKAT: Interval-Censored Sequence Kernel Association Test
Implements the Interval-Censored Sequence Kernel Association (ICSKAT) test for testing the association between interval-censored time-to-event outcomes and groups of single nucleotide polymorphisms (SNPs). Interval-censored time-to-event data occur when the event time is not known exactly but can be deduced to fall within a given interval. For example, some medical conditions like bone mineral density deficiency are generally only diagnosed at clinical visits. If a patient goes for clinical checkups yearly and is diagnosed at, say, age 30, then the onset of the deficiency is only known to fall between the date of their age 29 checkup and the date of the age 30 checkup. Interval-censored data include right- and left-censored data as special cases. This package also implements the interval-censored Burden test and the ICSKATO test, which is the optimal combination of the ICSKAT and Burden tests. Please see the vignette for a quickstart guide.
Authors:
ICSKAT_0.2.0.tar.gz
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ICSKAT.pdf |ICSKAT.html✨
ICSKAT/json (API)
| # Install 'ICSKAT' in R: |
| install.packages('ICSKAT', repos = c('https://ryansunwork.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 years agofrom:54da1a1821
Exports:ACATcalcScoreStatschiSqMatchFastconstruct_interval_probscoxphFncreateIntfIntegratefIntegrateLiugen_IC_dataICsingleSNPICskatICSKAT_fit_nullICSKAT_fit_null_POICSKATOICSKATO_bootstrapICskatPOICSKATwrappermake_IC_dmatmatchVisitmixture_kurtosisQrhoICsingleSNPaltsurvregFn
Dependencies:cliCompQuadFormdplyrfansigenericsgluelatticelifecyclemagrittrMatrixpillarpkgconfigR6RcppRcppEigenrjerlangsurvivaltibbletidyselectutf8vctrswithrzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Aggregated Cauchy Association Test | ACAT |
| calcScoreStats.R | calcScoreStats |
| chiSqMatchFast.R | chiSqMatchFast |
| construct_interval_probs.R | construct_interval_probs |
| coxphFn | coxphFn |
| Called by gen_IC_data() to turn the actual outcome times and observation times into interval-censored outcomes for each subject. Apply this with mapply over a data.frame of visit times, pass in the exact times. | createInt |
| fIntegrate.R | fIntegrate |
| fIntegrateLiu.R | fIntegrateLiu |
| gen_IC_data.R | gen_IC_data |
| ICsingleSNP.R | ICsingleSNP |
| ICSKAT.R | ICskat |
| ICSKAT_fit_null.R | ICSKAT_fit_null |
| ICSKAT_fit_null_PO.R | ICSKAT_fit_null_PO |
| ICSKATO.R | ICSKATO |
| ICSKATO_bootstrap.R | ICSKATO_bootstrap |
| ICSKATPO.R | ICskatPO |
| ICSKATwrapper.R | ICSKATwrapper |
| make_IC_dmat.R | make_IC_dmat |
| match_visit.R | matchVisit |
| mixture_kurtosis.R | mixture_kurtosis |
| QrhoIC.R | QrhoIC |
| singleSNPalt.R | singleSNPalt |
| survregFn | survregFn |
