GWASdata-class function

S4 class for an object representing a Genome-wide Assocaition Study.

S4 class for an object representing a Genome-wide Assocaition Study.

'GWASdata' is a GWASdata object constructor.

show displays basic information on GWASdata object

summary summarizes the content of a GWASdata object and gives an overview about the information included in a GWASdata object. Summary statistics for phenotype and genotype data are calculated.

GeneSNPsize creates a data.frame of pathway

names with numbers of snps and genes in each pathway.

GWASdata(object, ...)

## S4 method for signature 'ANY'
GWASdata(geno, anno, pheno = NULL, desc = "")

## S4 method for signature 'GWASdata'
show(object)

## S4 method for signature 'GWASdata'
summary(object)

## S4 method for signature 'GWASdata'
GeneSNPsize(object)

Arguments

• object: A GWASdata object.
• ...: Further arguments can be added to the function.
• geno: An object of any type, including the genotype information.
• anno: A data.frame containing the annotation file for the GWASdata object.
• pheno: A data.frame specifying individual IDs, phenotypes and covariates to be included in the regression model.
• desc: A character giving the GWAS description, e.g. name of study.

Methods (by generic)

• GeneSNPsize(GWASdata): creates a data.frame of pathway names with numbers of snps and genes in each pathway.

Slots

• geno: An object of any type, including genotype information. The format needs to be one line per individual and on colum per SNP in minor-allele coding (0,1,2). Other values between 0 and 2, as from impute dosages, are allowed. Missing values must be imputed prior to creation of a GWASdata object.
• anno: A data.frame mapping SNPs to genes and genes to pathways. Needs to include the columns 'pathway' (pathway ID, e.g. hsa number from KEGG database), 'gene' (gene name (hgnc_symbol)), 'chr' (chromosome), 'snp' (rsnumber) and 'position' (base pair position of SNP).
• pheno: A data.frame specifying individual IDs, phenotypes and covariates to be included in the regression model e.g. ID, pheno, sex, pack.years. Note: IDs have to be in the first column!
• desc: A character giving the GWAS description, e.g. name of study.

Examples

# create gwas data object
data(pheno)
data(geno)
data(anno)
gwas <- new('GWASdata', pheno=pheno, geno=geno, anno=anno, desc="some study") 
# show and summary methods
gwas
summary(gwas)
# SNPs and genes in pathway
GeneSNPsize(gwas)

Author(s)

Juliane Manitz, Stefanie Friedrichs