Package: Summix 2.11.0

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]

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Summix.pdf |Summix.html✨
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Peer review:

Bug tracker:https://github.com/bioconductor/summix/issues

On BioConductor:Summix-2.11.0(bioc 3.20)Summix-2.10.0(bioc 3.19)

bioconductor-package

15 exports 1.00 score 67 dependencies

Last updated 2 months agofrom:0ee06a7345

Exports:adjAFadjAF_calccalc_effective_Ncalc_scaledObjdoInternalSimulationgetNextEndPointgetNextStartPointsaveBlocksizeGetNextsummixsummix_calcsummix_localsummix_networktestDiffvariantGetNext

Dependencies:base64encbbmlebdsmatrixBEDASSLEbslibcachemcliclustercodacolorspacecurldigestdplyremdbookevaluatefansifarverfastmapfontawesomefsgenericsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmatrixcalcmemoisemimemunsellmvtnormnloptrnumDerivpillarpkgconfigplyrR6randomcoloRrappdirsRColorBrewerRcpprlangrmarkdownRtsnesassscalesstringistringrtibbletidyselecttinytexutf8V8vctrsviridisLitevisNetworkwithrxfunyaml