position_filter: Remove positions outside of window
In AbbVie-ComputationalGenomics/POEMColoc: Implement POEM colocalization method

Description Usage Arguments Details Examples

Remove positions outside of window

1	position_filter(dataset_list, window_size)

`dataset_list`	list of 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
`window_size`	non-negative integer giving the window around the top SNP to retain (setting to 1 will include 1 base on either side, not including the SNP itself) if set to NULL, will retain all positions

keeps any positions within window size of any top SNP in dataset_list. in the event that the windows do not completely overlap, it retains all positions in between.

dataset_empty <- 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))
dataset_empty2 <- list(pos = integer(0), MAF = numeric(0), N=1000, type ="quant", beta = numeric(0), varbeta = numeric(0), chr= "Z", imputation_class = "top", top_pos = 2, snp = character(0))
# should warn
position_filter(list(dataset_empty, dataset_empty2), window_size = NULL)
# 2 empty sets should stay empty
position_filter(list(dataset_empty, dataset_empty2), window_size = 10^10)
# empty set and full set should be governed by full
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))
position_filter(list(dataset_empty, dataset_empty2, dataset_full), window_size = NULL)
position_filter(list(dataset_empty, dataset_empty2, dataset_full), window_size = 1)
position_filter(list(dataset_empty, dataset_empty2, dataset_full), window_size = 0)
# Different top SNP positions should include everything in between them
dataset_full2 <- 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(1, 4 * 10^-8, 2 * 10^-4, 0.6, 2 * 10^-8), chr= "Z", imputation_class = "all", top_pos = 5, snp = as.character(1:5))
dataset_full3 <- list(pos = c(2, 3, 4), MAF = c(0.15, 0.25, 0.2), N=1000, type ="quant", pvalues = c(4 * 10^-8, 2 * 10^-4, 0.6), chr= "Z", imputation_class = "all", top_pos = 2, snp = as.character(2:4))
position_filter(list(dataset_empty, dataset_empty2, dataset_full3, dataset_full2), window_size = 0)
position_filter(list(dataset_empty, dataset_empty2, dataset_full3, dataset_full2), window_size = 10)
# should warn
dataset_top_SNP <- dataset_full
dataset_top_SNP2 <- dataset_full2
dataset_top_SNP$imputation_class = "top"
dataset_top_SNP2$imputation_class = "top"
position_filter(list(dataset_empty, dataset_empty2, dataset_top_SNP, dataset_top_SNP2), window_size = NULL)
# should run without warning
position_filter(list(dataset_empty, dataset_empty2, dataset_top_SNP, dataset_top_SNP2), window_size = 10)