CollapsABEL (version 0.10.11)

plGwas: Constructor for PlGwasC class

Description

Constructor for PlGwasC class

Usage

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

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)