R/tanimotoCoef.R

In LittleHeronCodes/Lazy2: Lazy Package

#' Tanimoto coefficients
#'
#' Calculates Tanimoto coefficients (Jaccard Index) given two set vectors.
#' @param A set input1 as vectors
#' @param B set input2 as vectors
#' @param T background space (if given, A and B are intersected with T before calculating, causing the function to run slower)
#' @examples
#' A <- c(1:5)
#' B <- c(3:7)
#' tanimotoCoef(A, B)
#' @export

tanimotoCoef <- function(A, B, T = NULL) {
    if (!is.null(T)) {
        A <- intersect(A, T)
        B <- intersect(B, T)
    }
    int <- intersect(A, B)
    uni <- union(A, B)
    return(length(int) / length(uni))
}


#' Calculate Enrichment factor
#'
#' Enrichment factor represents the "enrichment" of overlap between two sets in a given space.
#' This is calculated as (observed count) / (expected count).
#' @param setA set input1 as vectors
#' @param setB set input2 as vectors
#' @param setT total set as vectors
#' @param psc pseudocount for when expected count is too low.
#' @examples
#' A <- c(1:5)
#' B <- c(3:7)
#' total <- c(1:10)
#' getEnrichmentFactor(A, B, total)
#' @export

getEnrichmentFactor <- function(setA, setB, setT, psc = 0) {
    setA <- intersect(setA, setT)
    setB <- intersect(setB, setT)

    ef <- NA
    A <- length(setA)
    B <- length(setB)
    T <- length(setT)
    I <- length(intersect(setA, setB))
    if ((A / T * B) != 0) {
        ef <- (I + psc) / (A / T * B + psc)
    }
    return(ef)
}


#' Hypergeometric test
#'
#' Run one-tailed hypergeometric test (fisher test) with set inputs.
#' 'hypergeoTest' uses hypergeometric distribution function phyper with lower.tail = FALSE fixed.
#' This is commonly used for testing significance in overlap between sets.
#'
#' @param query     query set        (balls drawn)
#' @param reference reference set    (white balls)
#' @param bgspace   background space (balls in urn)
#' @return Returns a dataframe of 4 columns. pVal is p value returned by phyper.
#' oddsRatio gives number of observation by number of expectation. int and bg refers to
#' the number of intersected items and background space respectively.
#' By nature of phyper, reference and query input should be interchangeable.
#' @export

hypergeoTest <- function(query, reference, bgspace) {
    query <- intersect(query, bgspace)
    reference <- intersect(reference, bgspace)

    N <- length(bgspace) # no of balls in urn
    k <- length(query) # no of balls drawn from urn (DEG no)
    m <- length(reference) # no of white balls in urn
    q <- length(intersect(reference, query)) # no of white balls drawn

    pVal <- phyper(q - 1, m, N - m, k, lower.tail = FALSE)
    odds <- (q / k) / (m / N)
    return(data.frame(pVal = pVal, oddsRatio = odds, int = q, bg = N))
}


#' Harmonic Mean
#'
#' Calculate harmonic mean. Harmonic means are often used to calculate means of p-values.
#' @param v numeric vector
#' @param ... further arguments to be passed to or from methods
#' @export
#' @examples
#' v <- seq(0.01, .99, .01)
#' harmean(v)
harmean <- function(v, ...) {
    1 / mean(1 / v, ...)
}