summary.GGInetwork: Printing summaries class '"GGInetwork"' objects

Description Usage Arguments Details Value Examples

View source: R/summary.GGInetwork.R

Description

Printing summaries for objects of class "GGInetwork"

Usage

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## 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

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## 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)

MathieuEmily/GeneGeneInteR documentation built on May 7, 2019, 3:42 p.m.