snps_to_condition: Identify SNPs to condition on

In RajLabMSSM/echolocatoR: Automated genomic fine-mapping

Identify SNPs to condition on

Description

When running conditional analyses (e.g. GCTA-COJO), this functions automatically identifies SNP to condition on.

Usage

snps_to_condition(conditioned_snps, topSNPs, loci)

Arguments

conditioned_snps	Which SNPs to conditions on when fine-mapping with (e.g. COJO).
topSNPs	A data.frame with the genomic coordinates of the lead SNP for each locus. The lead SNP will be used as the center of the window when extracting subset from the full GWAS/QTL summary statistics file. Only one SNP per Locus should be included. At minimum, topSNPs should include the following columns: Locus A unique name for each locus. Often, loci are named after a relevant gene (e.g. LRRK2) or based on the name/coordinates of the lead SNP (e.g. locus_chr12_40734202) CHR The chromosome that the SNP is on. Can be "chr12" or "12" format. POS The genomic position of the SNP (in basepairs)
loci	Character list of loci in Locus col of topSNPs.

Value

Vector of SNPs

RajLabMSSM/echolocatoR documentation built on Jan. 29, 2023, 6:04 a.m.