add_metadata: Add some additional fields to datasets
In AbbVie-ComputationalGenomics/POEMColoc: Implement POEM colocalization method

Description Usage Arguments Value Examples

Add some additional fields to datasets

1	add_metadata(dataset)

dataset

list of datasets formatted according to the requirements of coloc.abf with the following differences pos, and chr are additionally required. snp is ignored as it is determined by pos. For top SNP datasets, R2 and MAF and gds_file and subset are optional, if supplied as arguments to the function. For full summary statistic datasets, MAF is required.

list of datasets with the following additions snp is created from pos top_pos is created as the position of the lowest p-value imputation_class either all or top indicating if imputation is needed.

# p-value input
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")
dataset_top_SNP <- list(pos = 2, N= 10000, s =0.5, type="cc", pvalues = 10^-9, chr = "Z")
add_metadata(dataset_full)
add_metadata(dataset_top_SNP)
# beta-varbeta input
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$varbeta = c(0.009, 0.008, 0.012, 0.01, 0.015)
dataset_full_beta_varbeta$sdY = 1
dataset_top_SNP_beta <- list(pos = 2, N= 10000, s =0.5, type="cc", beta = 2, varbeta = 0.05, chr = "Z")
add_metadata(dataset_full_beta_varbeta)
add_metadata(dataset = dataset_top_SNP_beta)