mash_set_data: Create a data object for mash analysis.

In mashr: Multivariate Adaptive Shrinkage

Create a data object for mash analysis.

Description

Create a data object for mash analysis.

Usage

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 N] 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

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

mashr documentation built on Oct. 18, 2023, 5:08 p.m.