plGwas: Constructor for PlGwasC class

In CollapsABEL: Generalized CDH (GCDH) Analysis

Description

Constructor for PlGwasC class

Usage

plGwas(pl_gwas, pheno, pheno_name, covar_name, gwas_tag, assoc, opts)


  ## S4 method for signature 
## 'PlGwasC,character,character,character,character,logical,list'
plGwas(pl_gwas,
  pheno, pheno_name, covar_name, gwas_tag, assoc, opts)


  ## S4 method for signature 
## 'RbedInfoC,character,character,character,character,logical,list'
plGwas(pl_gwas,
  pheno, pheno_name, covar_name, gwas_tag, assoc, opts)


  ## S4 method for signature 
## 'RbedInfoC,character,character,character,character,missing,missing'
plGwas(pl_gwas,
  pheno, pheno_name, covar_name, gwas_tag, assoc, opts)


  ## S4 method for signature 
## 'RbedInfoC,character,character,character,character,missing,list'
plGwas(pl_gwas,
  pheno, pheno_name, covar_name, gwas_tag, assoc, opts)


  ## S4 method for signature 
## 'RbedInfoC,character,character,character,character,logical,missing'
plGwas(pl_gwas,
  pheno, pheno_name, covar_name, gwas_tag, assoc, opts)


  ## S4 method for signature 
## 'RbedInfoC,character,character,missing,character,missing,missing'
plGwas(pl_gwas,
  pheno, pheno_name, covar_name, gwas_tag, assoc, opts)

Arguments

pl_gwas	PlGwasC or PlInfoC object
pheno	character. Phenotype file
pheno_name	character. Phenotype names.
covar_name	character. Covariate names.
gwas_tag	character. Tag for this GWAS.
assoc	logical. Whether use the "–assoc" option for PLINK.
opts	list. Options to be passed to PLINK.

Value

PlGwasC object

Author(s)

Kaiyin Zhong, Fan Liu

Examples

## Not run: 
gwas_tag = "mmp13_page_sex_age"
rbed_info = rbedInfo(bedstem = "mmp13")
pl_gwas = plGwas(rbed_info, 
		pheno = "mmp13.phe",
		pheno_name = "Page", 
		covar_name = "Sex,Cage", 
		gwas_tag = gwas_tag)
runGwas(pl_gwas)
"mmp13_page_sex_age" %in% listGwasTags() == "TRUE"
gwas_out = readGwasOut(pl_gwas, rmGwasOut = FALSE)
colClasses(gwas_out) == c("integer", "character", "integer", 
    "character", "character", "integer", 
    "numeric", "numeric", "numeric")

## End(Not run)

CollapsABEL documentation built on May 1, 2019, 7:28 p.m.