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Note: Manuscript of the package entitled as "solarius: an R interface to SOLAR for variance component analysis in pedigrees" is under revision in Bioinformatics journal.
R package wrapper to SOLAR
library(devtools)
install_github("ugcd/solarius")
SOLAR
has already automatedSOLAR
from system.call with options
and settings
parametersdata.frame
salamboR
artifacts (ancestor of solarius
)SOLAR
SOLAR
artifacts# load library
library(solarius)
# load data set for running polygenic and linkage models
data(dat30)
# univariate polygenic model
mod1 <- solarPolygenic(trait1 ~ age + sex, dat30, covtest = TRUE)
# bivariate polygenic model
mod2 <- solarPolygenic(trait1 + trait2 ~ 1, dat30,
polygenic.options = '-testrhoe -testrhog')
# specify directory with IBD matrices and run linkage model
mibddir <- system.file('extdata', 'solarOutput',
'solarMibdsCsv', package = 'solarius')
link <- solarMultipoint(trait1 ~ 1, dat30,
mibddir = mibddir, chr = 5)
# load data set and run association model in parallel
data(dat50)
assoc <- solarAssoc(trait ~ age + sex, phenodata,
kinship = kin, snpdata = genodata, cores = 2)
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