dataset_filter: Remove positions from dataset

In AbbVie-ComputationalGenomics/POEMColoc: Implement POEM colocalization method

Description

Remove positions from dataset

Usage

dataset_filter(dataset, keep)

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
keep	vector of length L with positions to keep

Value

POEM_output format dataset

Examples

# example with p-values
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))
dataset_filter(dataset = dataset_full, c(TRUE, FALSE, FALSE, TRUE, FALSE))
dataset_filter(dataset = dataset_full, rep(TRUE,5))
dataset_filter(dataset = dataset_full, rep(FALSE,5))
# example with beta
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
dataset_filter(dataset = dataset_full_beta_varbeta, c(TRUE, FALSE, FALSE, TRUE, FALSE))
dataset_filter(dataset = dataset_full_beta_varbeta, rep(TRUE,5))
dataset_filter(dataset = dataset_full_beta_varbeta, rep(FALSE,5))
# example with empty that should be TRUE
dataset_empty <- list(pos = integer(0), MAF = numeric(0), N=1000, type ="quant", pvalues = numeric(0), chr= "Z", imputation_class = "all", top_pos = 1, snp = character(0))
dataset_filter(dataset = dataset_empty, logical())

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