diagplot.ftd {metaseqR} | R Documentation

## Create False (or True) Positive (or Negative) curves

### Description

This function creates false (or true) discovery curves using a matrix of p-values (such a matrix can be derived for example from the result table of `metaseqr` by subsetting the table to get the p-values from several algorithms) given a ground truth vector for differential expression.

### Usage

        diagplot.ftd(truth, p, type = "fpc", N = 2000,
            output = "x11", path = NULL, draw = TRUE, ...)

### 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. The elements of `truth` MUST be named (e.g. each gene's name).
`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. The p-values MUST be named (e.g. each gene's name).
`type` | what to plot, can be `"fpc"` for False Positive Curves (default), `"tpc"` for True Positive Curves, `"fnc"` for False Negative Curves or `"tnc"` for True Negative Curves.
`N` | create the curves based on the top (or bottom) `N` ranked genes (default is 2000) to be used with `type="fpc"` or `type="tpc"`.
`output` | one or more R plotting device to direct the plot result to. Supported mechanisms: `"x11"` (default), `"png"`, `"jpg"`, `"bmp"`, `"pdf"` or `"ps"`.
`path` | the path to create output files.
`draw` | boolean to determine whether to plot the curves or just return the calculated values (in cases where the user wants the output for later averaging for example). Defaults to `TRUE` (make plots).
`...` | further arguments to be passed to plot devices, such as parameter from `par`.

### Value

A named list with two members: the first member (`ftdr`) contains the values used to create the plot. The second member (`path`) contains the path to the created figure graphic.

### 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)
    ftd.obj <- diagplot.ftd(truth,p,N=100)

[Package metaseqR version 1.26.0 Index]