Error checks and plotting speedups for dive_phe2mash function

man/get_pairwise_sharing.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mash-evaluation.R
+\name{get_pairwise_sharing}
+\alias{get_pairwise_sharing}
+\title{Compute the proportion of (significant) signals shared by magnitude in each pair of conditions, based on the poterior mean}
+\usage{
+get_pairwise_sharing(m, factor = 0.5, lfsr_thresh = 0.05, FUN = identity)
+}
+\arguments{
+\item{m}{the mash fit}
+
+\item{factor}{a number between 0 and 1 - the factor within which effects are
+considered to be shared.}
+
+\item{lfsr_thresh}{the lfsr threshold for including an effect in the
+assessment}
+
+\item{FUN}{a function to be applied to the estimated effect sizes before
+assessing sharing. The most obvious choice beside the default
+'FUN=identity' would be 'FUN=abs' if you want to ignore the sign of the
+effects when assesing sharing.}
+}
+\description{
+Compute the proportion of (significant) signals shared by magnitude in each pair of conditions, based on the poterior mean
+}
+\details{
+For each pair of tissues, first identify the effects that are
+significant (by lfsr<lfsr_thresh) in at least one of the two tissues.
+Then compute what fraction of these have an estimated (posterior mean)
+effect size within a factor \code{factor} of one another. The results are
+returned as an R by R matrix.
+}
+\examples{
+\dontrun{
+get_pairwise_sharing(m) # sharing by magnitude (same sign)
+get_pairwise_sharing(m, factor=0) # sharing by sign
+get_pairwise_sharing(m, FUN=abs) # sharing by magnitude when sign is ignored
+}
+
+}