geneSNP {geneNR} | R Documentation |
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")
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) |
Value
A data frame containing traits, SNP, gene_id, gene_size, and gene_type.
Examples
load(system.file("extdata", "precomputed_sample_results.rda", package = "geneNR"))
message(sample_results)
result <- geneSNP("sample_data_wheat", 10000, 10000, crop = "wheat")
result <- geneSNP("sample_data_rice", 10000, 10000, crop = "rice")
[Package geneNR version 2.0.1 Index]