assign_SNPs_to_genes: Assign SNPs to genes

In PAST: Pathway Association Study Tool (PAST)

Description

Assign SNPs to genes

Usage

assign_SNPs_to_genes(
  gwas_data,
  LD,
  gff_file,
  filter_type,
  window,
  r_squared_cutoff,
  num_cores
)

Arguments

gwas_data	Merged association and effects data from merge_data()
LD	Linkage disequilibrium data from parse_LD()
gff_file	The path to a GFF file
window	The search window for genes around the SNP
r_squared_cutoff	The R^2 value used to determine SNP significance
num_cores	The number of cores to use in parallelizing PAST

Value

A dataframe of genes from the SNP data

Examples

example("load_GWAS_data")
example("load_LD")
demo_genes_file = system.file("extdata", "genes.gff",
  package = "PAST", mustWork = TRUE)
filter_type = c("gene")
genes <-assign_SNPs_to_genes(gwas_data, LD, demo_genes_file, filter_type, 1000, 0.8, 2)

PAST documentation built on Nov. 8, 2020, 8:31 p.m.