assign_SNPs_to_genes {PAST}R Documentation

Assign SNPs to genes

Description

Assign SNPs to genes

Usage

assign_SNPs_to_genes(gwas_data, LD, gff_file, 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)
genes <-assign_SNPs_to_genes(gwas_data, LD, demo_genes_file, 1000, 0.8, 2)

[Package PAST version 1.0.0 Index]