GWASdata | R Documentation |
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)
object |
A |
... |
Further arguments can be added to the function. |
geno |
An object of any type, including the genotype information. |
anno |
A |
pheno |
A |
desc |
A |
GeneSNPsize(GWASdata)
: creates a data.frame
of pathway
names with numbers
of snps and genes in each pathway.
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.
Juliane Manitz, Stefanie Friedrichs
# 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)
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