get_pheno_variance: Compute phenotype variance

In RajLabMSSM/echofinemap: echoverse module: Fine-mapping functions

Compute phenotype variance

Description

Compute phenotype variance (var_y in susieR).

Usage

get_pheno_variance(dat, case_control, var_y, verbose = TRUE)

Arguments

dat	Fine-mapping results data.
case_control	Whether the summary statistics come from a case-control study (e.g. a GWAS of having Alzheimer's Disease or not) (TRUE) or a quantitative study (e.g. a GWAS of height, or an eQTL) (FALSE).
var_y	[Optional] User-supplied phenotypic variance value(s). Can be one of the following: NULL: Variance will be inferred automatically by SUSIE. Numeric vector: Variance will be computed directly from vector. Character string: The name of a column in dat to extract a numeric vector from to compute variance. "case_control"Variance will be inferred from the proportion of cases/controls in the study. Only works when both "N_cases" and "N_controls" are columns in dat.
verbose	Print messages.

RajLabMSSM/echofinemap documentation built on Jan. 3, 2023, 1:42 a.m.