dNdS_segment: dNdS_segment

In vivaldi: Viral Variant Location and Diversity

dNdS_segment

Description

Reads in a dataframe that has been arranged (arrange_data), filtered (filter_variants), and annotated (prepare_annotations), calculates dNdS, and outputs plots

Usage

dNdS_segment(annotation_df, SPLICEFORMS)

Arguments

annotation_df	A rearranged, filtered, and annotated vcf dataframe - must be for amino-acid specific calculations, cannot be the same as the dataframe used for SNP calculations
SPLICEFORMS	A character vector of isoform names

Value

A plot showing the dN/dS ratio for each splice form (rather than segment) for each sample

Examples

# Sample Data
head(example_filtered_SNV_df)
dim(example_filtered_SNV_df)

# Plot showing the dN/dS ratio for each splice form
SPLICEFORMS = c("H1N1_PB2.1", "H1N1_PB1.1","H1N1_NS.2")
dNdS_segment(example_filtered_SNV_df, SPLICEFORMS)

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