empty_dataset_check: check if empty dataset

In AbbVie-ComputationalGenomics/POEMColoc: Implement POEM colocalization method

Description

check if empty dataset

Usage

empty_dataset_check(dataset)

Arguments

dataset

POEM_output format dataset Specifically this is a coloc format dataset with the following changes top_pos giving the position of the top p-value pos vector giving positions chr giving chromosome snp is mandatory MAF is mandatory imputation class that is either all or top Unlike coloc, length of pvalues or beta L is permitted to be zero

Value

TRUE or FALSE

Examples

# example with p-values that should be FALSE
dataset_full <- list(pos = c(1, 2, 3, 4, 5), MAF = c(0.14, 0.15, 0.25, 0.2, 0.4), N=1000, type ="quant", pvalues = c(2 * 10^-8, 4 * 10^-8, 2 * 10^-4, 0.6, 0.03), chr= "Z", imputation_class = "all", top_pos = 1, snp = as.character(1:5))
empty_dataset_check(dataset = dataset_full)
# example with beta that should be FALSE
dataset_full_beta_varbeta = dataset_full
dataset_full_beta_varbeta$pvalues = NULL
dataset_full_beta_varbeta$beta = c(0.5, 0.5, 0.4, 0.5, 0.26)
dataset_full_beta_varbeta$varbeta = c(0.008, 0.008, 0.012, 0.01, 0.015)
dataset_full_beta_varbeta$sdY = 1
empty_dataset_check(dataset = dataset_full_beta_varbeta)
# example with p-values that should be TRUE
dataset_empty <- list(pos = integer(0), MAF = numeric(0), N=1000, type ="quant", pvalues = numeric(0), chr= "Z", imputation_class = "top", top_pos = 1, snp = character(0))
empty_dataset_check(dataset = dataset_empty)
# example with beta that should be TRUE
dataset_empty <- list(pos = integer(0), MAF = numeric(0), N=1000, type ="quant", beta = numeric(0), varbeta = numeric(0), chr= "Z", imputation_class = "top", top_pos = 1, snp = character(0))
empty_dataset_check(dataset = dataset_empty)

AbbVie-ComputationalGenomics/POEMColoc documentation built on May 20, 2020, 12:32 a.m.