calc_SNPindex: Calculate SNP-index

In EG-lisy/BSAvis: Bulk Segregant Analysis - Visualisation Package

Description

This function calculates, for both wild-type and mutant bulks, the SNP-index value of each variant stored inside the data frame (returned by the readBSA_vcf() function), applying the following formula:

SNPindex=AD_alt/(AD_ref + AD_alt)

Bulks get joined together in a single data frame.

Note that the user can select specific variants to consider, by setting the "variants" parameter to "SNP" (default) or "all" (InDels+SNPs).

Usage

calc_SNPindex(vcf.df, wtBulk, mBulk, variants = "SNP")

Arguments

vcf.df	Data frame of the vcf file
wtBulk	Wild-Type pool
mBulk	Mutant pool
variants	variants to be considered. Default is "SNP" (allowed: "SNP" or "all")

Details

The data frame returned by readBSA_vcf() is filtered by bulk ID to create two separate data frames: one specific to the wild-type bulk variants information and other one specific to the mutant bulk variants information. For every variant in each data frame, the SNP-index value gets calculated and added as a new column.

In the instance that the type of variants to be considered is set to "SNP",the variants corresponding to InDel sare discarded. The rows containing more than three characters in the GT_alleles column (e.g.,"T/AT"corresponds to an insertion and contains 4 characters) or containing three characters but one of them being "*", meaning a deletion, are removed from the data frame.

Both dataframes are then joined by same chromosome and position to ensure that all the merged rows contain information on the same genomic position. This data frame is returned by the function

Value

Data frame containing variand and SNP-index information for each bulk.

Examples

## Calculate SNP-index for both bulks (only SNPs will be considered)
vcf_df_SNPindex <- calc_SNPindex(vcf.df=vcf_list$df, 
                                 wtBulk="pool_S3781_minus", 
                                 mBulk="pool_S3781_plus") 

## Calculate SNP-index considering both InDels and SNPs
vcf_df_SNPindex <- calc_SNPindex(vcf.df=vcf_list$df, 
                                 wtBulk="pool_S3781_minus", 
                                 mBulk="pool_S3781_plus",
                                 variants="all") 

EG-lisy/BSAvis documentation built on Dec. 17, 2021, 5:38 p.m.