calc.otr {metaseqR} | R Documentation

## Calculate the ratio TP/(FP+FN)

### Description

This function calculates the ratio of True Positives to the sum of False Positives and False Negatives given a matrix of p-values (one for each statistical test used) and a vector of ground truth (DE or non-DE). This function serves as a method evaluation helper.

### Usage

        calc.otr(truth, p, sig = 0.05)

### Arguments

`truth` | the ground truth differential expression vector. It should contain only zero and non-zero elements, with zero denoting non-differentially expressed genes and non-zero, differentially expressed genes. Such a vector can be obtained for example by using the `make.sim.data.sd` function, which creates simulated RNA-Seq read counts based on real data. It MUST be named with gene names, the same as in `p`.
`p` | a p-value matrix whose rows correspond to each element in the `truth` vector. If the matrix has a `colnames` attribute, a legend will be added to the plot using these names, else a set of column names will be auto-generated. `p` can also be a list or a data frame. In any case, each row (or element) MUST be named with gene names (the same as in `truth`).
`sig` | a significance level (0 < `sig` <=1).

### Value

A named list with two members. The first member is a data frame with the numbers used to calculate the TP/(FP+FN) ratio and the second member is the ratio TP/(FP+FN) for each statistical test.

### Author(s)

Panagiotis Moulos

### Examples

    p1 <- 0.001*matrix(runif(300),100,3)
    p2 <- matrix(runif(300),100,3)
    p <- rbind(p1,p2)
    rownames(p) <- paste("gene",1:200,sep="_")
    colnames(p) <- paste("method",1:3,sep="_")
    truth <- c(rep(1,40),rep(-1,40),rep(0,20),rep(1,10),
        rep(2,10),rep(0,80))
    names(truth) <- rownames(p)
    otr <- calc.otr(truth,p)

[Package metaseqR version 1.20.0 Index]