run.univ.bivar: Perform both univariate and bivariate tests, with filtering...

In josefin-werme/LAVA: Local Analysis of [co]Variant Association

Perform both univariate and bivariate tests, with filtering based on univariate signal

Description

Will only perform bivariate test for all phenotypes that pass the univariate significance threshold. By default, the bivariate test will be performed for all combinations of phenotypes in the locus, but this can be modified using the 'phenos' and 'target' arguments (see below)

Usage

run.univ.bivar(
  locus,
  phenos = NULL,
  target = NULL,
  univ.thresh = 0.05,
  adap.thresh = c(1e-04, 1e-06),
  p.values = T,
  CIs = T,
  param.lim = 1.25
)

Arguments

locus	Locus object created using the the process.locus function. Contains all the relevant parameters and processed sum-stats for the phenotypes of interest
phenos	Subset of phenotypes to analyse, and/or their order. If NULL, all phenotypes in the locus object will be analysed (in the order listed within the locus object)
target	Target phenotype of interest. If NULL, bivariate correlations between all pairs of phenotypes will be computed; Otherwise, this will only be done between the target phenotype and all other phenotypes.
univ.thresh	P-value threshold for the univariate test, used to determine whether phenotypes exhibit sufficient local heritability for a bivariate test
adap.thresh	The thresholds at which to increase the number of iterations for the p-value generation. Default number of iterations is 1e+4, but will be increased to 1e+5, and 1e+6 as p-values fall below the respective thresholds. If set to NULL, the maximum number of iterations is capped at the default (Note: this significantly speeds up the analysis, but results in poor accuracy for low p-values)
p.values	Set to F to suppress p-values
CIs	Set to F to suppress 95% confidence intervals
param.lim	The +- threshold at which estimated parameters are considered to be too far out of bounds. If the estimated parameter exceeds this threshold, it is considered unreliable and will be set to NA.

Value

List containing the results from the univariate and bivariate tests (see ?run.univ() and ?run.bivar() for more info)

josefin-werme/LAVA documentation built on July 4, 2024, 8:11 p.m.