SPAGE.one.SNP: SaddlePoint Approximation implementation of GxE analysis...

Description Usage Arguments Value Examples

View source: R/main.R

Description

One-SNP-version SPAGE function. This function is to facilitate users that prefer reading and analyzing genotype line-by-line.

Usage

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SPAGE.one.SNP(g, obj.null, Envn.mtx, Cutoff = 2,
  impute.method = "none", missing.cutoff = 0.15, min.maf = 0,
  Firth.cutoff = 0, BetaG.cutoff = 0.001, BetaG.SPA = F,
  G.Model = "Add")

Arguments

g

a numeric genotype vector. Missing genotype should be coded as NA. Both hard-called and imputed genotype data are supported.

others

the same as function SPAGE. NOTE that we do not check subject order in this one-snp-version !!!

Value

the same as function SPAGE.

Examples

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Data.ls = data.simu.null(N = 1000, nSNP = 10, nCov = 2, maf = 0.3, prev = 0.1)
Phen.mtx = Data.ls$Phen.mtx
obj.null = SPAGE_Null_Model(y~Cov1+Cov2, data=Phen.mtx, out_type="D")
Envn.mtx = Data.ls$Phen.mtx[,"Cov1",drop=FALSE]
## Check help(SPAGE) to better understand the output?
SPAGE.one.SNP(Data.ls$Geno.mtx[,"rs1"], obj.null, Envn.mtx)

WenjianBI/SPAGE documentation built on Nov. 13, 2020, 12:15 p.m.