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Last data update: 2014.03.03

R: Display functions for local fdr output

summary.fdr.result

R Documentation

Display functions for local fdr output

Description

Display functions for output from fdr1d and fdr2d, summarizing the output, displaying the proportion of non-differentially expressed genes and extracting the list of top-regulated genes.

Usage

summary.fdr.result(object, ...)

p0(x, how = FALSE)

topDE(x, co = 0.1)

Arguments

`x, object`	an object of class `fdr.result` created by `fdr1d` or `fdr2d`.
`how`	a logical value indicating whether to return only the numerical value of the proportion of non-differentially expressed genes, or a list whose second element indicates whether the proportion was estimated from the data or supplied by the user.
`...`	extra arguments, currently unused
`co`	cutoff for either FDR or fdr

Value

For summary.fdr.result, a list with the summary items.

For p0, either a numerical value or a list with two elements, depending on the value of parameter how.

For topDE, the genes that have FDR (EOC) or fdr (fdr1d, fdr2d) less or equal than co, sorted by FDR or fdr respectively.

Author(s)

A. Ploner

Examples

# Create object res1d
example(fdr1d)

summary(res1d)
p0(res1d)
p0(res1d, how=TRUE)
topDE(res1d)

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.
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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(OCplus)
Loading required package: akima
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/OCplus/summary.fdr.result.Rd_%03d_medium.png", width=480, height=480)
> ### Name: summary.fdr.result
> ### Title: Display functions for local fdr output
> ### Aliases: summary.fdr.result p0 topDE
> ### Keywords: print utilities
> 
> ### ** Examples
> 
> # Create object res1d
> example(fdr1d)

fdr1d> # We simulate a small example with 5 percent regulated genes and
fdr1d> # a rather large effect size
fdr1d> set.seed(2000)

fdr1d> xdat = matrix(rnorm(50000), nrow=1000)

fdr1d> xdat[1:25, 1:25] = xdat[1:25, 1:25] - 1

fdr1d> xdat[26:50, 1:25] = xdat[26:50, 1:25] + 1

fdr1d> grp = rep(c("Sample A","Sample B"), c(25,25))

fdr1d> # A default run
fdr1d> res1d = fdr1d(xdat, grp)
Starting permutations...
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Smoothing f
Smoothing f0

fdr1d> res1d[1:20,]
       tstat   fdr.local
1  -3.113975 0.343518819
2  -4.868530 0.005661948
3  -4.487968 0.014988680
4  -3.891546 0.067078413
5  -2.323968 0.794599504
6  -2.491116 0.697740540
7  -2.896670 0.460201903
8  -4.254195 0.026995885
9  -3.490224 0.170529676
10 -3.465717 0.180666869
11 -2.642704 0.605687562
12 -1.532776 0.976587492
13 -3.805811 0.082774181
14 -4.138912 0.035586709
15 -4.999346 0.004067203
16 -3.724595 0.098722065
17 -4.853666 0.005843152
18 -2.607185 0.627256785
19 -3.639713 0.123482696
20 -4.881803 0.005500135

fdr1d> # Looking at the results
fdr1d> summary(res1d)
$Statistic
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
-5.247000 -0.647800 -0.003438  0.015690  0.736200  5.126000 

$fdr
         fdr
statistic (0,0.05] (0.05,0.1] (0.1,0.2] (0.2,1] (1,Inf]
     t<0         8          2         6     480       0
     t>=0       11          3         3     487       0

$p0
$p0$Value
[1] 0.8879223

$p0$Estimated
[1] TRUE



fdr1d> plot(res1d)

fdr1d> res1d[res1d$fdr<0.05, ]
        tstat   fdr.local
2   -4.868530 0.005661948
3   -4.487968 0.014988680
8   -4.254195 0.026995885
14  -4.138912 0.035586709
15  -4.999346 0.004067203
17  -4.853666 0.005843152
20  -4.881803 0.005500135
21  -4.273400 0.025780390
22  -5.247257 0.002150341
23  -4.550108 0.012704082
24  -5.002789 0.004025231
28   4.027545 0.035205867
30   4.274270 0.018487088
32   3.913886 0.047579527
37   4.810875 0.004376113
38   5.125711 0.001711363
39   4.883544 0.003480536
41   4.404355 0.013438726
522  4.017566 0.036292167

fdr1d> # Averaging estimates the global FDR for a set of genes
fdr1d> ndx = abs(res1d$tstat) > 3

fdr1d> mean(res1d$fdr[ndx])
[1] 0.08513626

fdr1d> # Extra information
fdr1d> class(res1d)
[1] "fdr1d.result" "fdr.result"   "data.frame"  

fdr1d> attr(res1d,"param")
$p0
[1] 0.8879223

$p0.est
[1] TRUE

$fdr
 [1] 0.002150341 0.003679441 0.006313912 0.010908497 0.018853690 0.032531021
 [7] 0.056260686 0.095823210 0.158862377 0.248254978 0.357555584 0.474579801
[13] 0.598819090 0.730049134 0.852474483 0.928910674 0.961551113 0.977649650
[19] 0.972012961 0.963954436 0.944227575 0.925816181 0.879585482 0.875265249
[25] 0.881280571 0.936401140 0.976673462 1.000000000 0.995431165 0.965258323
[31] 0.930756968 0.906137071 0.900032160 0.843371879 0.769103282 0.673382987
[37] 0.559230197 0.442600785 0.334090209 0.232379026 0.150794383 0.094266063
[43] 0.056810882 0.033284476 0.018990523 0.010603980 0.005822593 0.003159320
[49] 0.001711363

$xbreaks
 [1] -5.35530881 -5.13920530 -4.92310180 -4.70699829 -4.49089478 -4.27479127
 [7] -4.05868776 -3.84258426 -3.62648075 -3.41037724 -3.19427373 -2.97817022
[13] -2.76206672 -2.54596321 -2.32985970 -2.11375619 -1.89765268 -1.68154918
[19] -1.46544567 -1.24934216 -1.03323865 -0.81713514 -0.60103164 -0.38492813
[25] -0.16882462  0.04727889  0.26338240  0.47948590  0.69558941  0.91169292
[31]  1.12779643  1.34389994  1.56000344  1.77610695  1.99221046  2.20831397
[37]  2.42441748  2.64052098  2.85662449  3.07272800  3.28883151  3.50493502
[43]  3.72103852  3.93714203  4.15324554  4.36934905  4.58545256  4.80155606
[49]  5.01765957  5.23376308

> 
> summary(res1d)
$Statistic
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
-5.247000 -0.647800 -0.003438  0.015690  0.736200  5.126000 

$fdr
         fdr
statistic (0,0.05] (0.05,0.1] (0.1,0.2] (0.2,1] (1,Inf]
     t<0         8          2         6     480       0
     t>=0       11          3         3     487       0

$p0
$p0$Value
[1] 0.8879223

$p0$Estimated
[1] TRUE


> p0(res1d)
[1] 0.8879223
> p0(res1d, how=TRUE)
$Value
[1] 0.8879223

$Estimated
[1] TRUE

> topDE(res1d)
        tstat   fdr.local
38   5.125711 0.001711363
22  -5.247257 0.002150341
39   4.883544 0.003480536
24  -5.002789 0.004025231
15  -4.999346 0.004067203
37   4.810875 0.004376113
20  -4.881803 0.005500135
2   -4.868530 0.005661948
17  -4.853666 0.005843152
23  -4.550108 0.012704082
41   4.404355 0.013438726
3   -4.487968 0.014988680
30   4.274270 0.018487088
21  -4.273400 0.025780390
8   -4.254195 0.026995885
28   4.027545 0.035205867
14  -4.138912 0.035586709
522  4.017566 0.036292167
32   3.913886 0.047579527
35   3.774064 0.066348044
4   -3.891546 0.067078413
31   3.687758 0.081306609
13  -3.805811 0.082774181
16  -3.724595 0.098722065
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>