summary.GGInetwork {GeneGeneInteR} | R Documentation |
"GGInetwork"
objectsPrinting summaries for objects of class "GGInetwork"
## S3 method for class 'GGInetwork' summary(object, ...)
object |
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... |
further arguments passed to or from other methods |
summary.GGItest
provides a customized summary of a GGInetwork
object.
The form of the value returned by summary
depends on the class of its argument.
## Not run: ## Dataset is included in the package ped <- system.file("extdata/example.ped", package="GeneGeneInteR") info <- system.file("extdata/example.info", package="GeneGeneInteR") posi <- system.file("extdata/example.txt", package="GeneGeneInteR") ## Importation of the genotypes data.imported <- importFile(file=ped, snps=info, pos=posi, pos.sep="\t") ## Filtering of the data: SNPs with MAF < 0.05 or p.value for HWE < 1e-3 or ## call rate < 0.9 are removed. data.scour <- snpMatrixScour(snpX=data.imported$snpX,genes.info=data.imported$genes.info, min.maf=0.05,min.eq=1e-3,call.rate=0.9) ## Imputation of the missing genotypes data.imputed <- imputeSnpMatrix(data.scour$snpX, genes.info = data.scour$genes.info) ## Importation of the phenotype resp <- system.file("extdata/response.txt", package="GeneGeneInteR") Y <- read.csv(resp, header=FALSE) ## plot of the interaction between the 17 genes with the CLD method -- can take a few minutes GGI.res <- GGI(Y=Y, snpX=dta$snpX, genes.info=dta$genes.info,method="CLD") plot(GGI.res,threshold=0.05) ## Selection of 12 genes among 17 data.select <- selectSnps(data.imputed$snpX, data.imputed$genes.info, c("bub3","CDSN","Gc","GLRX", "PADI1","PADI2","PADI4","PADI6","PRKD3","PSORS1C1","SERPINA1","SORBS1")) GGI.res <- GGI(Y=Y, snpX=data.select$snpX, genes.info=data.select$genes.info,method="PCA") ## End(Not run) ## Equivalent importation of the GGI.res object load(system.file("extdata/GGIRes.Rdata", package="GeneGeneInteR")) summary(GGI.res)