Create_complete_snp_data: Create Complete SNP data

In TomerAntman/VCFtoGWAS: Get GWAS out of VCF file

Create Complete SNP data

Description

Given a set of results for a GWAS analysis (trial+trait) and the relevant mapping information of the SNPs in the data - the function creates a dataframe with information about the SNPs the were identified as significant (can be saved as csv.

Usage

Create_complete_snp_data(GWAS_trial_snps, trait, mapping_info, genes_df)

Arguments

GWAS_trial_snps	SNPs from a certain GWAS trial (for example'GWAS_trial_snps <- GWAS$signSnp[[GWAS_trial_name]]')
trait	The desired trait (as was analysed in the GWAS)
mapping_info	The fixed information about the SNPs, linking between the unique names and the SNP's location and type.
genes_df	Dataframe that contains info about the genes (that the significant SNPs might be in). For yeast, there is an included file in the package data (SacCer_sgd_cds)

Details

The returned information includes attributes such as location in the genome and if the SNP happens to be located in a gene coding sequence, the dataframe also includes information about the gene and the alternated amino acid sequence

Value

SNP_information

The information as metioned in the description and in the details

Author(s)

Tomer Antman

References

Data source for CDS file extraction

To create the final dataframe used as input, I used ‘create_SacCer_sgd_cds.R’

TomerAntman/VCFtoGWAS documentation built on July 6, 2022, 4:51 a.m.