filter_SNPratio: Filter SNP-index Variants

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

Description

This functions allows to filter out bulk variants stored inside the data frame (returned by the calc_SNPratio() function) which do not fall between the minimumSNP-index, minimum DP and maximum DP.

Usage

filter_SNPratio(vcf.df.SNPratio, min.SNPratio = 0.1, min.DP = 50, max.DP = 200)

Arguments

vcf.df.SNPratio	vcf dataframe
min.SNPratio	min value allowed for the SNP index (default=0.1)
min.DP	min value allowed for the read depth (default=50)
max.DP	max value allowed for the read depth (default=200)

Details

Variants in the data frame returned by calc_SNPratio() with SNP-ratio values less below the minimum SNP-ratio value, as well as variants which do not fall between the given (or default) minimum and maximum DP values in both bulks, are discarded and removed from the final data frame returned by the function.

Value

Data frame containing filtered variant information.

Examples

## Default parameters
vcf_df_SNPratio_filt <- filter_SNPratio(vcf.df.SNPratio=vcf_df_SNPratio)
## Custom parameters
vcf_df_SNPratio_filt <- filter_SNPratio(vcf.df.SNPratio=vcf_df_SNPratio, 
                                        min.SNPratio=0.3, 
                                        min.DP=60, 
                                        max.DP=250)

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