Package: Summix 2.13.0

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:Audrey Hendricks [cre], Price Adelle [aut], Stoneman Haley [aut]

Summix_2.13.0.tar.gz
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Summix.pdf |Summix.html
Summix/json (API)
NEWS

# Install 'Summix' in R:
install.packages('Summix', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:Summix-2.13.0(bioc 3.21)Summix-2.12.0(bioc 3.20)

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

statisticalmethodwholegenomegenetics

4.75 score 14 scripts 170 downloads 15 exports 67 dependencies

Last updated 10 days agofrom:f89e6d584c. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winOKNov 12 2024
R-4.5-linuxOKNov 12 2024
R-4.4-winOKNov 12 2024
R-4.4-macOKNov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKNov 12 2024

Exports:adjAFadjAF_calccalc_effective_Ncalc_scaledObjdoInternalSimulationgetNextEndPointgetNextStartPointsaveBlocksizeGetNextsummixsummix_calcsummix_localsummix_networktestDiffvariantGetNext

Dependencies:base64encbbmlebdsmatrixBEDASSLEbslibcachemcliclustercodacolorspacecurldigestdplyremdbookevaluatefansifarverfastmapfontawesomefsgenericsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmatrixcalcmemoisemimemunsellmvtnormnloptrnumDerivpillarpkgconfigplyrR6randomcoloRrappdirsRColorBrewerRcpprlangrmarkdownRtsnesassscalesstringistringrtibbletidyselecttinytexutf8V8vctrsviridisLitevisNetworkwithrxfunyaml

Summix2

Rendered fromSummix.rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-04-23
Started: 2024-02-09

Readme and manuals

Help Manual

Help pageTopics
adjAFadjAF
adjAF_calcadjAF_calc
ancestryDataancestryData
calc_effective_Ncalc_effective_N
calc_scaledObjcalc_scaledObj
doInternalSimulationdoInternalSimulation
getNextEndPointgetNextEndPoint
getNextStartPointgetNextStartPoint
saveBlocksaveBlock
sizeGetNextsizeGetNext
summixsummix
summix_calcsummix_calc
summix_localsummix_local
summix_networksummix_network
testDifftestDiff
variantGetNextvariantGetNext