run.bivar: Bivariate local genetic correlation analysis

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

Bivariate local genetic correlation analysis

Description

Performs bivariate local genetic correlation analysis between two phenotypes. 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.bivar(
  locus,
  phenos = NULL,
  target = NULL,
  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. If NULL, all phenotypes in the locus object will be analysed
target	Target phenotype of interest. If NULL, bivariate correlations between all pairs of phenotypes will be computed; Otherwise, only the relations between the target phenotype and the other phenotypes will be tested.
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

Data frame with the columns:

• phen1 / phen2 - analysed phenotypes

• rho - standardised coefficient for the local genetic correlation

• rho.lower / rho.upper - 95% confidence intervals for rho

• r2 - proportion of variance in genetic signal for phen1 explained by phen2 (and vice versa)

• r2.lower / r2.upper - 95% confidence intervals for the r2

• p - simulation p-values for the local genetic correlation

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