calculate_entropy: Calculate entropy for a vector of transcript-level expression...
In esebesty/SplicingFactory: Splicing Diversity Analysis for Transcriptome Data

Description Usage Arguments Details Value Examples

Calculate entropy for a vector of transcript-level expression values of one gene.

1	calculate_entropy(x, norm = TRUE, pseudocount = 0)

`x`	Vector of expression values.
`norm`	If `TRUE`, the entropy values are normalized to the number of transcripts for each gene. The normalized entropy values are always between 0 and 1. If `FALSE`, genes cannot be compared to each other, due to possibly different maximum entropy values.
`pseudocount`	Pseudocount added to each transcript expression value. Default is 0, while Laplace entropy uses a pseudocount of 1.

The function calculates an entropy value as part of different diversity calculations. Given a vector of transcript-level expression values of a gene, this function characterizes the diversity of splicing isoforms for a gene. If there only a single transcript, the diversity value will be NaN, as it cannot be calculated. If the expression of the given gene is 0, the diversity value will be NA.

A single gene-level entropy value.

# read counts for the transcripts of a single gene with 5 transcripts
x <- rnbinom(5, size = 10, prob = 0.4)
# calculate non-normalized naive entropy value
entropy <- calculate_entropy(x, norm = FALSE)
# calculate Laplace-entropy, also normalized for transcript number
# (the default)
norm_laplace_entropy <- calculate_entropy(x, pseudocount = 1)