geneNR (version 2.0.1)

geneSNP: Identifies Candidate Genes based on identified Single Nucleotide Ploymorphisms (SNPs) from Genome Wide Association Stuides (GWAS) Analysis

Description

Identifies Candidate Genes based on identified Single Nucleotide Ploymorphisms (SNPs) from Genome Wide Association Stuides (GWAS) Analysis

Usage

geneSNP(data_file, upstream = 1e+06, downstream = 1e+06, crop = "wheat")

Value

A data frame containing traits, SNP, gene_id, gene_size, and gene_type.

Arguments

data_file

The input data in .csv format. (sample_data_wheat or sample_data_rice for demo purpose)

upstream

The search window upstream of the current position of the SNP. (default: 1000000)

downstream

The search window downstream of the current position of the SNP. (default: 1000000)

crop

Either "wheat" or "rice". (default: wheat)

Examples

load(system.file("extdata", "precomputed_sample_results.rda", package = "geneNR"))
message(sample_results)
# \donttest{
result <- geneSNP("sample_data_wheat", 10000, 10000, crop = "wheat")
result <- geneSNP("sample_data_rice", 10000, 10000, crop = "rice")
# }