sensitivity.plot: Sensitivity plot

In jrs95/hyprcoloc: Hypothesis Prioritisation in multi-trait Colocalization (HyPrColoc)

Sensitivity plot

Description

sensitivity.plot is a function which repeatedly calls the hyprcoloc function to compute a similarity matrix which illustrates how strongly clustered/colocalized pairs of traits are across different input thresholds and priors

Usage

sensitivity.plot(
  effect.est,
  effect.se,
  binary.outcomes = rep(0, dim(effect.est)[2]),
  trait.subset = c(1:dim(effect.est)[2]),
  trait.names = c(1:dim(effect.est)[2]),
  snp.id = c(1:dim(effect.est)[1]),
  ld.matrix = diag(1, dim(effect.est)[1], dim(effect.est)[1]),
  trait.cor = diag(1, dim(effect.est)[2], dim(effect.est)[2]),
  sample.overlap = matrix(rep(1, dim(effect.est)[2]^2), nrow = dim(effect.est)[2]),
  bb.alg = TRUE,
  bb.selection = "regional",
  reg.steps = 1,
  reg.thresh = c(0.6, 0.7, 0.8, 0.9),
  align.thresh = c(0.6, 0.7, 0.8, 0.9),
  prior.1 = 1e-04,
  prior.c = c(0.02, 0.01, 0.005),
  prior.12 = NULL,
  uniform.priors = FALSE,
  ind.traits = TRUE,
  equal.thresholds = FALSE,
  similarity.matrix = FALSE
)

Arguments

effect.est	matrix of snp regression coefficients (i.e. regression beta values) in the genomic region
effect.se	matrix of standard errors associated with the beta values
binary.outcomes	a binary vector of dimension the number of traits: 1 represents a binary trait 0 otherwise
trait.subset	vector of trait names (or number) from the full trait list: used for trageted colocalization analysis in a region
trait.names	vector of trait names corresponding to the columns in the effect.est matrix
snp.id	vector of SNP IDs
ld.matrix	LD matrix
trait.cor	matrix of pairwise correlations between traits
sample.overlap	matrix of pairwise sample overlap between traits
bb.alg	branch and bound algorithm: TRUE, employ BB algorithm; FALSE, do not
bb.selection	branch and bound algorithm type, e.g. regional or alignment selection
reg.steps	regional step paramter
reg.thresh	a vector of regional probability thresholds
align.thresh	a vector of alignment probability thresholds
prior.1	prior probability of a SNP being associated with one trait
prior.c	vector of conditional colocalization priors: where prior.c is the probability of a SNP being associated with an additional trait given that the SNP is associated with at least 1 other trait
prior.12	COLOC prior p12: prior probability of a SNP being associated with any two traits
uniform.priors	uniform priors
ind.traits	are the traits independent or to be treated as independent
equal.thresholds	fix the regional and alignment thresholds to be equal
similarity.matrix	To be viewed as a similarity matrix. Default FALSE.

Author(s)

Christopher Foley [e-mail] & James Staley [e-mail]

jrs95/hyprcoloc documentation built on April 10, 2024, 4:11 a.m.