summary.GGInetwork {GeneGeneInteR} | R Documentation

## Printing summaries class `"GGInetwork"` objects

### Description

Printing summaries for objects of class `"GGInetwork"`

### Usage

    ## S3 method for class 'GGInetwork'
    summary(object, ...)

### Arguments

`object` | `GGInetwork`. Given as output of `GGI`.
`...` | further arguments passed to or from other methods

### Details

`summary.GGItest` provides a customized summary of a `GGInetwork` object.

### Value

The form of the value returned by `summary` depends on the class of its argument.

### Examples

    ## 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)

[Package GeneGeneInteR version 1.12.0 Index]