GenotypeDataDS: Class GenotypeData.

In isglobal-brge/dsOmics: DataSHIELD server site Omic functions

Class GenotypeData.

Description

Container for storing genotype data from a GWAS together with the metadata associated with the subjects (e.g. phenotypes and covariates) and SNPs involved in the study. This is a wrapper of GenotypeData function from GWASTools package.

Usage

GenotypeDataDS(
  x,
  covars,
  columnId,
  sexId,
  male_encoding,
  female_encoding,
  case_control_column,
  case,
  control
)

Arguments

x	a GdsGenotypeReader object (see GWASTools). It is the object that is obtained in the opal servers from a resource of type VCF2GDS
covars	a data.frame or a tibble having the metadata of samples (i.e. phenotypes and/or covariates)
columnId	character Column of the covars that contains the IDs
sexId	character (default NULL) Column of the covars that contains the sex phenotype
male_encoding	character (default "male") String used to encode the male sex phenotype on the covars table
female_encoding	character (default "female") String used to encode the female sex phenotype on the covars table
case_control_column	character (default NULL) Column that holds the case/control to relevel to 0/1
case	character (default NULL) Encoding of the case of the case_control_column
control	character (default NULL) Encoding of the control of the case_control_column

Value

...

Author(s)

Gonzalez, JR.

isglobal-brge/dsOmics documentation built on March 22, 2023, 4:01 a.m.