mist: mist
In mcanouil/MiSTr: Mixed effects Score Test for continuous outcomes

mist	R Documentation

mist

Description

Test for association between a set of SNPS/genes and continuous outcomes by including variant characteristic information and using score statistics.

Usage

mist(
  y,
  X,
  G,
  Z,
  method = "liu",
  model = c("guess", "continuous", "binary"),
  weight.beta = NULL,
  maf = NULL
)

Arguments

`y`	[numeric] A `numeric` vector of the continuous outcome variables. Missing values are not allowed.
`X`	[numeric] A `numeric` matrix of covariates with rows for individuals and columns for covariates. If there is no covariate, it does not need to be specified
`G`	[numeric] A `numeric` genotype matrix with rows for individuals and columns for SNPs. Each SNP should be coded as 0, 1, and 2 for AA, Aa, aa, where A is a major allele and a is a minor allele. Missing genotypes are not allowed.
`Z`	[numeric] a `numeric` matrix of second level covariates for variant characteristics. Each row corresponds to a variant and each column corresponds to a variant characteristic. If there is no second level covariates, a vector of 1 should be used.
`method`	[character] A method to compute the p-value and the default value is "liu". Method "davies" represents an exact method that computes the p-value by inverting the characteristic function of the mixture chisq. Method "liu" represents an approximation method that matches the first 3 moments.
`model`	[character] A `character` vector specifying the model. Default is to `"guess"`. Possible choices are `"guess"`, `"continuous"` (linear regression) or `"binary"` (logistic regression).
`weight.beta`	[numeric] A `numeric` vector of parameters of beta function which is the weight for scorestatistics. The default value is `NULL`, i.e. no weight. Default weight value could be `c(1, 25)`.
`maf`	[numeric] A `numeric` vector of MAF (minor allele frequency) for each SNP.

Value

S.tau score Statistic for the variant heterogeneous effect.
S.pi score Statistic for the variant mean effect.
p.value.S.tau P-value for testing the variant heterogeneous effect.
p.value.S.pi P-value for testing the variant mean effect.
p.value.overall Overall p-value for testing the association between the set of SNPS/genes and outcomes. It combines p.value.S.pi and p.value.S.tau by using Fisher's procedure.

Examples


library(MiSTr)
data(mist_data)
attach(mist_data)

mist(
  y = phenotypes[, "y_taupi"],
  X = phenotypes[, paste0("x_cov", 0:2)],
  G = genotypes,
  Z = variants_info[, 1, drop = FALSE]
)

mist(
  y = phenotypes[, "y_binary"],
  X = phenotypes[, paste0("x_cov", 0:2)],
  G = genotypes,
  Z = variants_info[, 1, drop = FALSE]
)

mcanouil/MiSTr documentation built on April 7, 2023, 10:48 a.m.