diagplot.ftd {metaseqR} | R Documentation |
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.
diagplot.ftd(truth, p, type = "fpc", N = 2000, output = "x11", path = NULL, draw = TRUE, ...)
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
|
p |
a p-value matrix whose rows correspond
to each element in the |
type |
what to plot, can be |
N |
create the curves based on the
top (or bottom) |
output |
one or more R plotting device to
direct the plot result to. Supported mechanisms:
|
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 |
... |
further arguments to be passed to plot
devices, such as parameter from |
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.
Panagiotis Moulos
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)