clonality: Clonality

In davidcoffey/LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

Description

Creates a data frame giving the total number of sequences, number of unique productive sequences, number of genomes, entropy, clonality, Gini coefficient, and the frequency (%) of the top productive sequences in a list of sample data frames.

Usage

clonality(file.list)

Arguments

file.list

A list of data frames consisting of antigen receptor sequencing imported by the LymphoSeq function readImmunoSeq. "aminoAcid", "count", and "frequencyCount" are required columns. "estimatedNumberGenomes" is optional. Note that clonality is usually calculated from productive nucleotide sequences. Therefore, it is not recommended to run this function using a productive sequence list aggregated by amino acids.

Details

Clonality is derived from the Shannon entropy, which is calculated from the frequencies of all productive sequences divided by the logarithm of the total number of unique productive sequences. This normalized entropy value is then inverted (1 - normalized entropy) to produce the clonality metric.

The Gini coefficient is an alternative metric used to calculate repertoire diversity and is derived from the Lorenz curve. The Lorenz curve is drawn such that x-axis represents the cumulative percentage of unique sequences and the y-axis represents the cumulative percentage of reads. A line passing through the origin with a slope of 1 reflects equal frequencies of all clones. The Gini coefficient is the ratio of the area between the line of equality and the observed Lorenz curve over the total area under the line of equality. Both Gini coefficient and clonality are reported on a scale from 0 to 1 where 0 indicates all sequences have the same frequency and 1 indicates the repertoire is dominated by a single sequence.

Value

Returns a data frame giving the total number of sequences, number of unique productive sequences, number of genomes, clonality, Gini coefficient, and the frequency (%) of the top productive sequence in each sample.

See Also

lorenzCurve

Examples

file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")

file.list <- readImmunoSeq(path = file.path)

clonality(file.list = file.list)

davidcoffey/LymphoSeq documentation built on Dec. 31, 2019, 9:52 p.m.