output: github_document | Package Installation | Summix2 Functionalities | Example of Summix2 Workflow | An in depth look at all Summix2 functionalities | summix | summix() Input | summix() Output | adjAF | adjAF() Input | adjAF() Output | summix_local | summix_local() Input | summix_local() Output | Examples using toy data in the Summix package | A quick demo of summix() | A quick demo of adjAF() | A quick demo of summix_local()
Package: Summix 2.19.0
Audrey Hendricks
Summix: Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data
This package contains the Summix2 method for estimating and adjusting for substructure in genetic summary allele frequency data. The function summix() estimates reference group proportions using a mixture model. The adjAF() function produces adjusted allele frequencies for an observed group with reference group proportions matching a target individual or sample. The summix_local() function estimates local ancestry mixture proportions and performs selection scans in genetic summary data.
Authors:
Summix_2.19.0.tar.gz
Summix_2.19.0.zip(r-4.7)Summix_2.19.0.zip(r-4.6)Summix_2.19.0.zip(r-4.5)
Summix_2.19.0.tgz(r-4.6-any)Summix_2.19.0.tgz(r-4.5-any)
Summix_2.19.0.tar.gz(r-4.7-any)Summix_2.19.0.tar.gz(r-4.6-any)
Summix_2.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Summix/json (API)
| # Install 'Summix' in R: |
| install.packages('Summix', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- ancestryData - AncestryData
On BioConductor:Summix-2.19.0(bioc 3.24)Summix-2.18.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
statisticalmethodwholegenomegenetics
Last updated from:945d819a04. Checks:1 ERROR, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 215 | ||
| linux-devel-x86_64 | OK | 186 | ||
| source / vignettes | OK | 200 | ||
| linux-release-x86_64 | OK | 190 | ||
| macos-release-arm64 | OK | 96 | ||
| macos-oldrel-arm64 | OK | 97 | ||
| windows-devel | OK | 120 | ||
| windows-release | OK | 121 | ||
| windows-oldrel | OK | 105 | ||
| wasm-release | OK | 160 |
Exports:adjAFadjAF_calccalc_effective_Ncalc_scaledObjdoInternalSimulationgetNextEndPointgetNextStartPointsaveBlocksizeGetNextsummixsummix_calcsummix_localsummix_networktestDiffvariantGetNext
Dependencies:base64encbbmlebdsmatrixBEDASSLEbslibcachemcliclustercodacolorspacecurldigestdplyremdbookevaluatefarverfastmapfontawesomefsgenericsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmatrixcalcmemoisemimemvtnormnloptrnumDerivpillarpkgconfigplyrR6randomcoloRrappdirsRColorBrewerRcpprlangrmarkdownRtsnesassscalesstringistringrtibbletidyselecttinytexutf8V8vctrsviridisLitevisNetworkwithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| adjAF | adjAF |
| adjAF_calc | adjAF_calc |
| ancestryData | ancestryData |
| calc_effective_N | calc_effective_N |
| calc_scaledObj | calc_scaledObj |
| doInternalSimulation | doInternalSimulation |
| getNextEndPoint | getNextEndPoint |
| getNextStartPoint | getNextStartPoint |
| saveBlock | saveBlock |
| sizeGetNext | sizeGetNext |
| summix | summix |
| summix_calc | summix_calc |
| summix_local | summix_local |
| summix_network | summix_network |
| testDiff | testDiff |
| variantGetNext | variantGetNext |