Package 'geneNR'

Title: Automated Gene Identification for Post-GWAS Analysis
Description: Facilitates the post-Genome Wide Association Studies (GWAS) analysis of identifying candidate genes within user-defined search window, based on the identified Single Nucleotide Polymorphisms (SNPs) as given by Mazumder AK (2024) <doi:10.1038/s41598-024-66903-3>. It supports candidate gene analysis for wheat and rice. Just import your GWAS result as explained in the sample_data file and the function does all the manual search and retrieve candidate genes for you, while exporting the results into ready-to-use output.
Authors: Rajamani Nirmalaruban [aut, cre, cph], R. Suvitha [aut], Rajbir Yadav [aut], Meda Alekya [aut], Amit Kumar Mazumder [aut], Subramani Sugumar [aut], Prashanth babu [aut], Manjeet Kumar [aut], Kiran B Gaikwad [aut], Naresh Kumar Bainsla [aut], S. Bhaskar Reddy [aut]
Maintainer: Rajamani Nirmalaruban <[email protected]>
License: CC BY 4.0
Version: 1.0.1
Built: 2025-03-11 07:23:46 UTC
Source: https://github.com/cran/geneNR

Help Index


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")

Sample Data

Description

A dataset containing sample data related to genetic markers and associated traits.

Usage

sample_data_rice

Format

A data frame with columns:

SNP

SNP identifier, character.

Chr

Chromosome location, character.

Pos

Position on the chromosome, numeric.

traits

Associated traits, character.

Source

Basha FTM, Sar P, Bhowmick PK, Mahato A, Bisht DS, Iquebal MA, Chakraborty K, Banerjee A, Verma BC, Bhaduri D, Kumar J, Ngangkham U, Saha S, Priyamedha, Mandal NP, Roy S. Genome-wide association study identified QTLs and genes underlying early seedling vigour in aus rice (Oryza sativa L.). Mol Genet Genomics. 2024 Dec 3;299(1):112. doi: 10.1007/s00438-024-02204-8. PMID: 39625651.

Examples

data(sample_data_rice)    #lazy loading

Sample Data

Description

A dataset containing sample data related to genetic markers and associated traits.

Usage

sample_data_wheat

Format

A data frame with columns:

SNP

SNP identifier, character.

Chr

Chromosome location, character.

Pos

Position on the chromosome, numeric.

traits

Associated traits, character.

Source

Generated for demonstration purposes

Examples

data(sample_data_wheat)    #lazy loading