post: Compute posterior for association mapping

In mingjingsi/LPM: LPM (Latent Probit Model)

Description

Compute posterior for association mapping.

Usage

post(data, X = NULL, id, LPMfit)

Arguments

data	A list of dataframes which contains SNP IDs and p-values for the target GWASs, the length is the number of GWASs considered.
X	Design matrix of functional annotations without intercept, where row and column correspond to SNP and annotation, respectively. Default is NULL.
id	ID of the GWASs considered, the length can be 1, 2 and 3. For example, id = c(1, 3) means we consider the first and the third GWAS in data.
LPMfit	LPM model fit.

Details

post compute posterior for association mapping.

Value

If the length of id is 1, the value includes

posterior

The posteriors that each SNP is associated with the target GWAS.

If the length of id is 2, the value includes

post.joint	The posteriors that each SNP is associated with both the two target GWASs.
post.marginal1	The posteriors that each SNP is associated with only the first target GWAS.
post.marginal2	The posteriors that each SNP is associated with only the second target GWAS.

If the length of id is 2, the value includes

post.joint	The posteriors that each SNP is associated with all the three target GWASs.
post.marginal1	The posteriors that each SNP is associated with only the first target GWAS.
post.marginal2	The posteriors that each SNP is associated with only the second target GWAS.
post.marginal3	The posteriors that each SNP is associated with only the third target GWAS.
post.marginal12	The posteriors that each SNP is associated with both the first and the second target GWAS.
post.marginal13	The posteriors that each SNP is associated with both the first and the third target GWAS.
post.marginal23	The posteriors that each SNP is associated with both the second and the third target GWAS.

Author(s)

Jingsi Ming

See Also

LPM, assoc

Examples

data(ExampleData)

posterior1 <- post(ExampleData$data[1], X = ExampleData$X, id = 1, LPMfit)

posterior13 <- post(ExampleData$data[c(1, 3)], X = ExampleData$X, id = c(1, 3), LPMfit)

mingjingsi/LPM documentation built on April 2, 2020, 9:32 a.m.