diagplotFtd: Create False (or True) Positive (or Negative) curves

In pmoulos/metaseqR2-local: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

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 metaseqr2 by subsetting the table to get the p-values from several algorithms) given a ground truth vector for differential expression.

Usage

    diagplotFtd(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 makeSimDataSd 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)
ftdObj <- diagplotFtd(truth,p,N=100)

pmoulos/metaseqR2-local documentation built on May 21, 2024, 3:46 a.m.