merge_finemapping_results: Merge fine-mapping results from all loci

In RajLabMSSM/echodata: echoverse module: Fine-mapping data access and formatting

Merge fine-mapping results from all loci

Description

Gather fine-mapping results from echolocatoR across all loci and merge into a single data.frame.

Usage

merge_finemapping_results(
  dataset = file.path(tempdir(), "Data/GWAS"),
  minimum_support = 1,
  include_leadSNPs = TRUE,
  LD_reference = NULL,
  save_path = tempfile(fileext = "merged_results.csv.gz"),
  from_storage = TRUE,
  credset_thresh = 0.95,
  consensus_thresh = 2,
  exclude_methods = NULL,
  top_CS_only = FALSE,
  verbose = TRUE,
  nThread = 1
)

Arguments

dataset	Path to the folder you want to recursively search for results files within (e.g. "Data/GWAS/Nalls23andMe_2019"). Set this to a path that includes multiple subfolders if you want to gather results from multiple studies at once (e.g. "Data/GWAS").
minimum_support	Filter SNPs by the minimum number of fine-mapping tools that contained the SNP in their Credible Set.
include_leadSNPs	Include lead GWAS/QTL SNPs per locus (regardless of other filtering criterion).
LD_reference	LD reference to use: "1KGphase1" : 1000 Genomes Project Phase 1 (genome build: hg19). "1KGphase3" : 1000 Genomes Project Phase 3 (genome build: hg19). "UKB" : Pre-computed LD from a British European-decent subset of UK Biobank. Genome build : hg19 "<vcf_path>" : User-supplied path to a custom VCF file to compute LD matrix from. Accepted formats: .vcf / .vcf.gz / .vcf.bgz Genome build : defined by user with target_genome. "<matrix_path>" : User-supplied path to a pre-computed LD matrix Accepted formats: .rds / .rda / .csv / .tsv / .txt Genome build : defined by user with target_genome.
save_path	Path to save merged table to.
from_storage	Search for stored results files.
credset_thresh	The minimum mean Posterior Probability (across all fine-mapping methods used) of SNPs to be included in the "mean.CS" column.
consensus_thresh	The minimum number of fine-mapping tools in which a SNP is in the Credible Set in order to be included in the "Consensus_SNP" column.
exclude_methods	Exclude certain fine-mapping methods when estimating mean.CS and Consensus_SNP.
top_CS_only	Only include the top 1 CS per fine-mapping method.
verbose	Print messages.
nThread	Number of threads to parallelise across.

Examples

dataset <- get_Nalls2019_loci(return_dir = TRUE)
merged_DT <- merge_finemapping_results(dataset = dataset)

RajLabMSSM/echodata documentation built on Nov. 21, 2023, 8 a.m.