RepeatABEL: GWAS for Multiple Observations on Related Individuals

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Performs genome-wide association studies on individuals that are both related and have repeated measurements.

Author
Lars Ronnegard
Date of publication
2016-08-18 09:07:21
Maintainer
Lars Ronnegard <lrn@du.se>
License
GPL
Version
1.1

View on R-Forge

Man pages

compute.GRM
Computes a Genetic Relationship Matrix from a GenABEL object
constructV
Constructs the (co)variance matrix for y
Create_gwaa_scan
Creates a scan.gwaa object
flycatchers
10,000 SNPs from 849 collared flycatchers
gen.data
Example GenABEL data
Phen.Data
Example phenotype data
preFitModel
Fits a linear mixed model (without fixed SNP effects) and...
RepeatABEL-package
GWAS for repeated observations on related individuals
rGLS
GWAS for Studies having Repeated Measurements on Related...
simulate_PhenData
Simulation function for the RepeatABEL package.
SmoothSNPmatrix
Imputes column means to missing genotypes
thinned.flycatchers
10,000 SNPs from 200 collared flycatchers

Files in this package

RepeatABEL/ChangeLog
RepeatABEL/DESCRIPTION
RepeatABEL/NAMESPACE
RepeatABEL/R
RepeatABEL/R/Create_gwaa_scan.R
RepeatABEL/R/SmoothSNPmatrix.R
RepeatABEL/R/compute.GRM.R
RepeatABEL/R/constructV.R
RepeatABEL/R/preFitModel.R
RepeatABEL/R/rGLS.R
RepeatABEL/R/simulate_PhenData.R
RepeatABEL/build
RepeatABEL/build/vignette.rds
RepeatABEL/data
RepeatABEL/data/Phen.Data.rda
RepeatABEL/data/datalist
RepeatABEL/data/flycatchers.rda
RepeatABEL/data/gen.data.rda
RepeatABEL/data/thinned.flycatchers.rda
RepeatABEL/inst
RepeatABEL/inst/CITATION
RepeatABEL/inst/doc
RepeatABEL/inst/doc/RepeatABEL_vignette.R
RepeatABEL/inst/doc/RepeatABEL_vignette.Rnw
RepeatABEL/inst/doc/RepeatABEL_vignette.pdf
RepeatABEL/man
RepeatABEL/man/Create_gwaa_scan.Rd
RepeatABEL/man/Phen.Data.Rd
RepeatABEL/man/RepeatABEL-package.Rd
RepeatABEL/man/SmoothSNPmatrix.Rd
RepeatABEL/man/compute.GRM.Rd
RepeatABEL/man/constructV.Rd
RepeatABEL/man/flycatchers.Rd
RepeatABEL/man/gen.data.Rd
RepeatABEL/man/preFitModel.Rd
RepeatABEL/man/rGLS.Rd
RepeatABEL/man/simulate_PhenData.Rd
RepeatABEL/man/thinned.flycatchers.Rd
RepeatABEL/vignettes
RepeatABEL/vignettes/Figure_Manhattan.pdf
RepeatABEL/vignettes/RepeatABEL_vignette.Rnw
RepeatABEL/vignettes/marginnote
RepeatABEL/vignettes/marginnote/README
RepeatABEL/vignettes/marginnote/marginnote.dtx
RepeatABEL/vignettes/marginnote/marginnote.ins
RepeatABEL/vignettes/marginnote/marginnote.pdf
RepeatABEL/vignettes/marginnote/marginnote.sty