Description Usage Arguments Value Author(s) Examples
Constructor for PlGwasC class
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | 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)
|
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. |
PlGwasC object
Kaiyin Zhong, Fan Liu
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## 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)
|
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