Description Usage Arguments Value Author(s) Examples
View source: R/metaseqr.plot.R
This function creates false (or true) discovery
curves using a matrix of pvalues (such a matrix
can be derived for example from the result table
of metaseqr
by subsetting the table
to get the pvalues from several algorithms)
given a ground truth vector for differential
expression.
1 2  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 nonzero elements, with zero denoting
nondifferentially expressed genes and nonzero,
differentially expressed genes. Such a vector
can be obtained for example by using the

p 
a pvalue 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
1 2 3 4 5 6 7 8 9  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)

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