shannon_entropy: shannon_entropy

In vivaldi: Viral Variant Location and Diversity

shannon_entropy

Description

Takes a rearranged vcf dataframe and calculates the Shannon entropy

Usage

shannon_entropy(df, genome_size)

Arguments

df	A rearranged vcf dataframe (arrange_data)
genome_size	Size of whole genome being used

Details

Shannon entropy is a commonly used metric to describe the amount of genetic diversity in sequencing data. It is calculated by considering the frequency of the ALT and REF allele at every position and then summing those values over 1) a segment or 2) the entire genome. These values can then be normalized by sequence length (kb) in order to compare across different segments or samples.

Value

A dataframe with Shannon entropy/kb calculations for the chroms and entire genome

Examples

# Sample dataframe
df <- data.frame(sample = c("m1", "m2", "m1", "m2", "m1"),
                 CHROM = c("PB1", "PB1", "PB2", "PB2", "NP"),
                 minorfreq = c(0.010, 0.022, 0.043, 0.055, 0.011),
                 majorfreq = c(0.990, 0.978, 0.957, 0.945, 0.989),
                 SegmentSize = c(2280, 2280, 2274, 2274, 1809)
)

df

genome_size = 13133

# MOdify the dataframe to add 5 new columns of shannon entropy data:
# 1. shannon_ntpos
# 2. chrom_shannon
# 3. genome_shannon
# 4. shannon_chrom_perkb
# 5. genome_shannon_perkb
shannon_entropy(df, genome_size)

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