snpdata2solar: Export snp genotypes, genotype covariates and amp to SOLAR
Description
A list of functions allows to pass SNPs data from R to SOLAR.
Usage
snpdata2solar(mat, dir)
snpcovdata2solar(mat, dir, nGTypes = FALSE, out)
snpmap2solar(map, dir)
Arguments
mat
A matrix of genotypes or genotypes as covariates to be exported.
dir
A character with path where SOLAR files to be created.
nGTypes
Logical, whether a column nGTypes to be added to snp.genocov file.
The default value is FALSE.
out
(optional) A list, that contains the names for snp.genocov and snp.geno-list files.
This argument is internally used in solarAssoc function.
map
A data frame with annotation (map) information for SNPs.
Details
snpdata2solar function (1) exports the data set of genotypes stored
in mat itto SOLAR files, (2) runs solar command `snp load solar.gen`
to check the data is loaded ok; (3) if two output files were not created,
throws an error.
snpcovdata2solar function emulates the `snp load` SOLAR command.
Two output files are produced: `snp.genocov` and `snp.geno-list`.
The steps are the following: (1) add prefix `snp_` to SNP names;
(2) (optional) compute stats on # genotyped individuals (columns `nGTypes`);
(3) write data and metadata into files.
snpmap2solar function (1) separates data by chromosome;
(2) write the table into SOLAR map file;
(3) check if the map file is OK by running SOLAR command load map -basepair