GENESIS

Package: GENESIS
Type: Package
Title: GENetic EStimation and Inference in Structured samples
(GENESIS): Statistical methods for analyzing genetic data from
samples with population structure and/or relatedness
Version: 2.2.2
Date: 2016-4-1
Author: Matthew P. Conomos and Timothy Thornton
Maintainer: Matthew P. Conomos <mconomos@uw.edu>
Description: The GENESIS package provides methodology for estimating,
inferring, and accounting for population and pedigree structure
in genetic analyses. The current implementation provides
functions to perform PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate
(Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components
Analysis on genome-wide SNP data for the detection of population
structure in a sample that may contain known or cryptic relatedness.
Unlike standard PCA, PC-AiR accounts for relatedness in the sample
to provide accurate ancestry inference that is not confounded by
family structure. PC-Relate uses ancestry representative principal
components to adjust for population structure/ancestry and accurately
estimate measures of recent genetic relatedness such as kinship
coefficients, IBD sharing probabilities, and inbreeding coefficients.
Additionally, functions are provided to perform efficient variance
component estimation and mixed model association testing for both
quantitative and binary phenotypes.
License: GPL-3
Depends: GWASTools
Imports: Biobase, gdsfmt, graph
Suggests: SNPRelate, SeqArray, SeqVarTools, RUnit, BiocGenerics, knitr
VignetteBuilder: knitr
biocViews: SNP, GeneticVariability, Genetics, StatisticalMethod,
DimensionReduction, PrincipalComponent, GenomeWideAssociation,
QualityControl, BiocViews
NeedsCompilation: no
Packaged: 2016-05-16 05:18:52 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'GENESIS' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GENESIS'
    finding HTML links ... done
    GENESIS-package                         html  
    HapMap_ASW_MXL_KINGmat                  html  
    assocTestMM                             html  
Rd warning: /tmp/RtmpZ2VzRi/R.INSTALL542a310b1336/GENESIS/man/assocTestMM.Rd:61: missing file link 'GenotypeData'
Rd warning: /tmp/RtmpZ2VzRi/R.INSTALL542a310b1336/GENESIS/man/assocTestMM.Rd:61: missing file link 'MatrixGenotypeReader'
Rd warning: /tmp/RtmpZ2VzRi/R.INSTALL542a310b1336/GENESIS/man/assocTestMM.Rd:61: missing file link 'GdsGenotypeReader'
    fitNullMM                               html  
Rd warning: /tmp/RtmpZ2VzRi/R.INSTALL542a310b1336/GENESIS/man/fitNullMM.Rd:70: missing file link 'ScanAnnotationDataFrame'
    king2mat                                html  
    pcair                                   html  
Rd warning: /tmp/RtmpZ2VzRi/R.INSTALL542a310b1336/GENESIS/man/pcair.Rd:72: missing file link 'GenotypeData'
Rd warning: /tmp/RtmpZ2VzRi/R.INSTALL542a310b1336/GENESIS/man/pcair.Rd:72: missing file link 'MatrixGenotypeReader'
Rd warning: /tmp/RtmpZ2VzRi/R.INSTALL542a310b1336/GENESIS/man/pcair.Rd:72: missing file link 'GdsGenotypeReader'
    pcairPartition                          html  
    pcrelate                                html  
Rd warning: /tmp/RtmpZ2VzRi/R.INSTALL542a310b1336/GENESIS/man/pcrelate.Rd:64: missing file link 'GenotypeData'
Rd warning: /tmp/RtmpZ2VzRi/R.INSTALL542a310b1336/GENESIS/man/pcrelate.Rd:64: missing file link 'MatrixGenotypeReader'
Rd warning: /tmp/RtmpZ2VzRi/R.INSTALL542a310b1336/GENESIS/man/pcrelate.Rd:64: missing file link 'GdsGenotypeReader'
    pcrelateMakeGRM                         html  
    pcrelateReadInbreed                     html  
    pcrelateReadKinship                     html  
    plot.pcair                              html  
    varCompCI                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GENESIS)
Making 'packages.html' ... done