Create Complete SNP data

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

References

Data source for CDS file extraction

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

Author

Tomer Antman