MultiLoad {MultiABEL} | R Documentation |
The function imports GenABEL (gwaa.data class) or DatABEL (.fv*) data formats to perform multivariate test for each genetic variant.
MultiLoad(gwaa.data = NULL, phenofile = NULL, genofile = NULL, trait.cols, covariate.cols = NULL, cuts = 20, impute = TRUE, gaussianize = TRUE, ...)
gwaa.data |
An (optional) object of |
phenofile |
An (optional) plain text file contains phenotypic outcomes and covariates. |
genofile |
An (optional) object of |
trait.cols |
A vector (length > 1) giving the column indices of the phenotypes to be analyzed. |
covariate.cols |
An (optional) vector giving the column indices of the covariates to be included. |
cuts |
An integer telling how many pieces the genotype data matrix will be splitted for analyze. The value can be set depending on the memory size. The smaller the value is, potentially the faster the analysis will be. |
impute |
An (optional) logical argument telling whether missing genotypes should be imputed. |
gaussianize |
An (optional) logical argument telling whether the phenotypes should be gaussianized via inverse-Gaussian transformation. |
... |
not used. |
The function returns a list of cleaned statistics for subsequent, with class multi.loaded
.
Either gwaa.data
(for GenABEL data format) or the combination of
phenofile
and genofile
(for DatABEL data format) has to be provided.
If all are provided, only phenofile
and genofile
will be used. When using
DatABEL format input, individual IDs in phenofile
and genofile
have to match!
Xia Shen
Xia Shen, ..., Jim Wilson, Gordan Lauc, Yurii Aulchenko (2015). Multi-omic-variate analysis identified novel loci associated with compound N-Glycosylation of human Immunoglobulin G. Submitted.
## Not run: ## loading example gwaa.data in GenABEL require(GenABEL) data(ge03d2ex.clean) ## running multivariate GWAS for 3 traits: height, weight, bmi loaded <- MultiLoad(gwaa.data = ge03d2ex.clean, trait.cols = c(5, 6, 8), covariate.cols = c(2, 3)) ## converting the same dataset into DatABEL format files require(DatABEL) write.table(phdata(ge03d2ex.clean), 'pheno.txt', col.names = TRUE, row.names = TRUE, quote = FALSE, sep = '\t') geno <- as.double(ge03d2ex.clean) matrix2databel(geno, 'geno') ## running the multivariate GWAS again loaded <- MultiLoad(phenofile = 'pheno.txt', genofile = 'geno', trait.cols = c(5, 6, 8), covariate.cols = c(2, 3)) ## End(Not run)