mash_set_data: Create a data object for mash analysis.

Description Usage Arguments Value Examples

Description

Create a data object for mash analysis.

Usage

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mash_set_data(
  Bhat,
  Shat = NULL,
  alpha = 0,
  df = Inf,
  pval = NULL,
  V = diag(ncol(Bhat)),
  zero_check_tol = .Machine$double.eps,
  zero_Bhat_Shat_reset = 0,
  zero_Shat_reset = 0
)

Arguments

Bhat

An N by R matrix of observed estimates.

Shat

An N by R matrix of corresponding standard errors. Shat can be a scalar if all standard errors are equal. This is most useful if Bhat is a matrix of Z scores, so elements of Shat are all 1. Default is 1.

alpha

Numeric value of alpha parameter in the model. alpha = 0 for Exchangeable Effects (EE), alpha = 1 for Exchangeable Z-scores (EZ). Default is 0. Please refer to equation (3.2) of M. Stephens 2016, Biostatistics for a discussion on alpha.

df

An N by R matrix of corresponding degrees of freedom of the t-statistic Bhat/Shat. Can be a scalar if all degrees of freedom are equal. Default is inf (for large samples).

pval

An N by R matrix of p-values of t-statistic Bhat/Shat. Shat and df should not be specified when pval is provided.

V

an R by R matrix / [R x R x J] array of effect specific correlation matrix of error correlations; must be positive definite. [So Bhat_j distributed as N(B_j,diag(Shat_j) V_j diag(Shat_j)) where _j denotes the jth row of a matrix]. Defaults to identity.

zero_check_tol

a small positive number as threshold for Shat to be considered zero if any Shat is smaller or equal to this number.

zero_Bhat_Shat_reset

Replace zeros in Shat matrix to given value if the corresponding Bhat are also zeros.

zero_Shat_reset

Replace zeros in Shat matrix to given value.

Value

A data object for passing into mash functions.

Examples

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simdata = simple_sims(50,5,1)
data = mash_set_data(simdata$Bhat, simdata$Shat)

mashr documentation built on May 24, 2021, 1:06 a.m.