assign_SNPs_to_genes {PAST} | R Documentation |
Assign SNPs to genes
assign_SNPs_to_genes( gwas_data, LD, gff_file, filter_type, window, r_squared_cutoff, num_cores )
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 |
A dataframe of genes from the SNP data
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)