Association model

args(solarAssoc)

## function (formula, data, dir, kinship, traits, covlist = "1", 
##     snpdata, snpformat = "012", cores = 1, ..., verbose = 0) 
## NULL

snpformat	snpdata	dat.gen	genocov
”/”	{A/A, A/T, T/T}	as is snpdata	{0, 1, 2}
“012”	{0, 1, 2}	{1/1, 1/2, 2/2}	{0, 1, 2}
“0.1”	[0; 2]	skipped	as is in snpdata

`SOLAR` commands and files

Association analysis provided by solarius package via solarAssoc function is based on mga command of SOLAR. The following code shows an exact rules (selected in solarius) to conduct an association analysis on 2 cores in parallel.

> mod <- solarAssoc(trait ~ 1, phenodata, snpdata = genodata, kinship = kin, cores = 2)
> mod$solar$assoc$cmd
[[1]]
[1] "load pheno dat.phe"                                             
[2] "load model trait/null0.mod"                                     
[3] "outdir assoc1"                                                  
[4] "mga -files snp.genocov -snplists snp.geno-list1 -out assoc.out1"

[[2]]
[1] "load pheno dat.phe"                                             
[2] "load model trait/null0.mod"                                     
[3] "outdir assoc2"                                                  
[4] "mga -files snp.genocov -snplists snp.geno-list2 -out assoc.out2"

A list of specific SOLAR files are used in the calculations, as described in the following table.

`SOLAR` file	`solarAssoc` argument	Comments
genocov.files	Yes (alternative to `snpdata`)	Data files with genotype-covariates (e.g. file per chromosome)
genolist.file	No	Meta file with SNP names (internal file derived from genocov.files)
snplist.files	Yes (alternative to `snplist`)	Meta files with SNP names to analize
out.dirs	No	Output directories for association models like `mga.mod` (directory per core)
out.files	No	Output files to store association results (file per core)

Two files genocov.files and genolist.file are output files of a group of commands, that convert genotypes to covariates. These three commands are snp load dat.snp, snp covar -nohaplos, snp unload. See snpdata2solar function for more details.

Other three files snplist.file, out.dirs and out.files are custom files by solarius package to control association analysis (list of snps to be analyzed, parallel computation).

`SOLAR` file	Default value	Parallel computation on 2 cores
genocov.files	“snp.genocov”
genolist.file	“snp.geno-list”
snplist.file	“snp.geno-list”	“snp.geno-list1”, “snp.geno-list2”
out.dirs	“assoc”	“assoc1”, “assoc2”
out.files	“assoc.out”	“assoc.out1”, “assoc.out2”

Example of association model

data(dat50)

mod <- solarAssoc(trait ~ 1, phenodata, snpdata = genodata, kinship = kin)
head(mod$snpf)

##   SNP NAv      chi     pSNP      bSNP bSNPse   Varexp
## 1  s1  66 0.166224 0.683490  0.144854      0 0.001258
## 2  s2  66 0.851450 0.356142 -0.665254      0 0.080241
## 3  s3  66 0.839794 0.359456 -0.330617      0 0.000000
## 4  s4  66 0.182198 0.669491  0.073773      0 0.000000
## 5  s5  66 0.049818 0.823380  0.344516      0 0.007852
## 6  s6  66 2.882008 0.089574 -0.249210      0 0.051719

solarius