a method for the plot generic. It is designed for displaying plots of the
estimated FDR and the genes' classification when performing a Single Time
Point Analysis for detecting differentially expressed genes in gene
expression data.
Usage
## S3 method for class 'STP'
plot(x, FDR=TRUE, AC=TRUE, WARNINGS=FALSE, tp=NULL, ...)
Arguments
x
an object of class 'STP' as returned by function stp.
FDR
if TRUE, a plot of the estimated FDR is displayed.
AC
if TRUE, a plot of the differentially expressed genes in the
artificial components is displayed.
WARNINGS
if TRUE and if a BCa confidence upper bound was computed for
obtaining x, the threshold values for which an extreme order
statistic was used in the BCa computations are shown (these warnings
are produced in calls to boot.ci).
tp
a character string to be added at the end of the plot's title
(used for adding time points in plot.TC).
...
further arguments passed to or from other methods.
## Single time point analysis for 500 genes with 10 treatment
## replicates and 10 control replicates
n <- 500; p <- 20; p1 <- 10
des <- c(rep(1, p1), rep(2, (p-p1)))
mu <- as.matrix(rexp(n, rate=1))
Z <- t(apply(mu, 1, function(mui) rnorm(p, mean=mui, sd=1)))
### 5 up regulated genes
Z[1:5,1:p1] <- Z[1:5,1:p1] + 5
### 10 down regulated genes
Z[6:15,(p1+1):p] <- Z[6:15,(p1+1):p] + 4
resSTP <- stp(Z, des)
resSTP
plot(resSTP)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(acde)
Loading required package: boot
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/acde/plot.STP.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.STP
> ### Title: Plot Method for Single Time Point Analysis
> ### Aliases: plot.STP
>
> ### ** Examples
>
> ## Single time point analysis for 500 genes with 10 treatment
> ## replicates and 10 control replicates
> n <- 500; p <- 20; p1 <- 10
> des <- c(rep(1, p1), rep(2, (p-p1)))
> mu <- as.matrix(rexp(n, rate=1))
> Z <- t(apply(mu, 1, function(mui) rnorm(p, mean=mui, sd=1)))
> ### 5 up regulated genes
> Z[1:5,1:p1] <- Z[1:5,1:p1] + 5
> ### 10 down regulated genes
> Z[6:15,(p1+1):p] <- Z[6:15,(p1+1):p] + 4
>
> resSTP <- stp(Z, des)
> resSTP
Single time point analysis for detecting differentially
expressed genes in microarray data.
Achieved FDR: 0.1%.
Inertia ratio: %.
tstar: 5.417, pi0: 1, B: 100.
Differentially expressed genes:
down-reg. no-diff. up-reg.
10 485 5
Results:
psi1 psi2 Q-value Diff. expr.
1 4.748 7.535 0.000 up-reg.
2 4.930 7.441 0.000 up-reg.
3 9.929 7.842 0.000 up-reg.
4 8.186 7.966 0.000 up-reg.
5 6.997 7.088 0.000 up-reg.
6 2.570 -6.477 0.000 down-reg.
7 4.180 -5.613 0.000 down-reg.
8 2.259 -6.747 0.000 down-reg.
9 3.753 -6.680 0.000 down-reg.
10 4.684 -6.152 0.000 down-reg.
11 9.927 -6.801 0.000 down-reg.
12 3.805 -5.623 0.000 down-reg.
13 8.216 -5.584 0.001 down-reg.
14 4.810 -5.528 0.001 down-reg.
15 3.117 -5.417 0.001 down-reg.
16 -0.281 2.086 0.272 no-diff.
17 -0.891 2.028 0.292 no-diff.
18 3.228 -1.905 0.351 no-diff.
19 -1.788 -1.512 0.583 no-diff.
20 -0.646 1.519 0.583 no-diff.
21 3.840 1.637 0.583 no-diff.
22 -2.025 1.587 0.583 no-diff.
23 6.355 1.663 0.583 no-diff.
24 -0.203 -1.528 0.583 no-diff.
25 1.900 1.679 0.583 no-diff.
...
*More results are available in the objects:
$ac, $qvalues and $dgenes.
> plot(resSTP)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
