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solarius (version 0.2.3)

An R Interface to SOLAR

Description

SOLAR is the standard software program to perform linkage and association mappings of the quantitative trait loci (QTLs) in pedigrees of arbitrary size and complexity. This package allows the user to exploit the variance component methods implemented in SOLAR. It automates such routine operations as formatting pedigree and phenotype data. It also parses the model output and contains summary and plotting functions for exploration of the results. In addition, solarius enables parallel computing of the linkage and association analyses, that makes the calculation of genome-wide scans more efficient. See for more information about SOLAR.

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Install

install.packages('solarius')

Monthly Downloads

8

Version

0.2.3

License

GPL (>= 3)

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Maintainer

Andrey Ziyatdinov

Last Published

May 9th, 2015

Functions in solarius (0.2.3)

getFormulaStr

Get formula string from a solarPolygenic object
df2solar

Export phenotype and pedigree data into SOLAR files
availableTransforms

Get a list of available transforms.
matchIdNames

Match ID column names
annotate

Annotate SNPs in association study
solarReadFiles

Read SOLAR output files in a directory
annotateSNPs

Annotate SNPs
solarMultipointClass

S3 class solarMultipoint.
plotKinship2

Plot the double kinship matrix
transformTrait

Transform a trait.
plotRes

Plot the residuals of a polygenic model
snpdata2solar

Export snp genotypes, genotype covariates and amp to SOLAR
solarAssocClass

S3 class solarAssoc.
plotPed

Plot the pedigree
solarPolygenic

Run polygenic analysis.
transformData

Apply transforms to a data set.
loadExamplesPhen

Load the example data (GAW10) from SOLAR.
matchMapNames

Match map column names
loadMulticPhen

Load the complete data set from R package multic
package.file

Alternative to system.file
solarMultipoint

Run multipoint linkage analysis.
readPhen

Read plain-text table files phen and ped
solarAssoc

Run association analysis.
solarKinship2

Compute empirical double kinship matrix by SOLAR
plotManh

Plot the association results
solar

Call SOLAR program from R
dat30

dat30 data set adapted from multic R package
solarPolygenicClass

S3 class solarPolygenic.
solariusPackage

solarius: an R package wrapper to SOLAR.
phenodata

dat50 data set adapted from FFBSKAT R package