calc_SNPratio: Calculate SNP-ratio

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

Description

This function allows to calculate the SNP-ratio between two bulks (M/WT), as follows:

(AD_ref.WT/(AD_ref.WT + AD_alt.WT)) - (AD_ref.M/(AD_ref.M + AD_alt.M))

Calculated SNP-ratio values get added in a new column of the data frame (returned by the readBSA_vcf() function). Note that the user can select specific variants to consider, by setting the "Variants" parameter to "SNP" (default) or "all" (respectively referring to SNPs or InDels+SNPs).

Usage

calc_SNPratio(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. In the case the type of variants is set to "SNP", variants corresponding to InDels are discarded by removing the rows in the data frame containing more than three characters in the GT_alleles column (e.g.,"T/AT"corresponds to an insertion and contains 4 characters). This also applies for deletions, where one of the three characters is a "*". Then, both data frames (wild-type bulk and mutant bulk) are joined by rows having the same value in the chromosome and position columns. The SNP-ratio is then calculated for each of the variants and the values are added in a new column of the joint data frame, which will be returned by the function.

Value

Data frame containing filtered variant and SNP-ratio information.

References

Wachsman et al., 2017

Examples

## Calculate SNP-index for both bulks (only SNPs will be considered)
vcf_df_SNPratio <- calc_SNPratio(vcf.df=vcf_list$df, 
                                 wtBulk="pool_S3781_minus", 
                                 mBulk="pool_S3781_plus") 
## Calculate SNP-index considering both InDels and SNPs
vcf_df_SNPratio <- calc_SNPratio(vcf.df=vcf_list$df, 
                                 wtBulk="pool_S3781_minus", 
                                 mBulk="pool_S3781_plus", 
                                 variants="all")

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