get_posterior_condition_wise_summary: Condition-wise Posterior Summary

In stephenslab/mashr: Multivariate Adaptive Shrinkage

Condition-wise Posterior Summary

Description

Provide condition-wise summary based on posterior distributions for each effect.

Usage

get_posterior_condition_wise_summary(mash_data, m, contrast_mat)

Arguments

mash_data	A mash data object, e.g. as created by mash_set_data
m	A mash fit, typically an output from mash.
contrast_mat	A matrix applied to mashr fitting result, enabling comparisons for different conditions based on posteior distributions.

Value

See compute_posterior_matrices_common_cov_R.

Examples

# The following example performs pairwise comparisons in a data set
# with 5 conditions: that is, it compares conditions (column) 1 and
# 2, 1 and 3, 1 and 4, 1 and 5, 2 and 3, etc.
library(Matrix)
set.seed(1)
simdata <- simple_sims(100,5,1)
dat <- mash_set_data(simdata$Bhat,simdata$Shat)
U <- cov_canonical(dat)
m <- mash(dat,U)
x <- combn(5,2)
n <- ncol(x)
contrast_mat <- as.matrix(sparseMatrix(i = rep(1:n,each = 2),
                                       j = as.vector(x),
                                       x = 1,dims = c(n,5)))
res <- get_posterior_condition_wise_summary(dat,m,contrast_mat)

stephenslab/mashr documentation built on Nov. 9, 2024, 12:29 a.m.