shared_snv_table: shared_snv_table

In vivaldi: Viral Variant Location and Diversity

shared_snv_table

Description

Reads in a dataframe that has been arranged (arrange_data) and filtered (filter_variants) and outputs a table

Usage

shared_snv_table(vardf)

Arguments

vardf

A rearranged (arrange_data) and filtered (filtered_variants) vcf dataframe

Details

The 'shared_snv_table()' function takes the variant dataframe and creates a new table, listing the variants in descending order of frequency how many samples they are found in. This function is meant to simplify further investigation of visual patterns in the previous plot.

Value

A table listing variants in order by how many samples they are found in

Examples

# Sample dataframe has 57 columns
dim(example_filtered_SNV_df)

# Simplify sample dataframe
df <- shared_snv_table(example_filtered_SNV_df)

# Dataframe created has 15 columns
df
dim(df)

vivaldi documentation built on March 31, 2023, 9:20 p.m.