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Last data update: 2014.03.03

R: Summary of a ROTS object

summary.ROTS

R Documentation

Summary of a ROTS object

Description

Summarizes the differential testing results from ROTS package.

Usage

  ## S3 method for class 'ROTS'
summary(object, fdr=NULL, num.genes=NULL, verbose=TRUE, ...)

Arguments

`object`	a `ROTS` object created from differential expression testing run by ROTS.
`fdr`	selected cutoff for FDR value.
`num.genes`	selected cutoff number for number of differentially detected features.
`verbose`	If TRUE (default), summary function will print out 10 first detections which fulfill the cutoff criteria.
`...`	other arguments passed to the summary function.

Details

This function returns the summary information (including row number, test-statistic, pvalue and FDR value) for the selected features.

Value

Returns a matrix where the rows are the selected features and columns are the Row number, ROTS-statistic, pvalue and FDR.

Author(s)

Fatemeh Seyednasrollah, Tomi Suomi, Laura L. Elo

Maintainer: Fatemeh Seyednasrollah <fatsey@utu.fi>

References

L. L. Elo, S. Filen, R. Lahesmaa and T. Aittokallio: Reproducibility-optimized test statistic for ranking genes in microarray studies. IEEE/ACM Transactions on Computational Biology and Bioinformatics 5: 423–431, 2008.

Examples

  ## ROTS-statistic for the Affymetrix spike-in data. 
  rots.out <- ROTS(data = affySpikeIn, groups = c(rep(0,5), rep(1,5)),
      B = 100, K = 500 , seed = 1234)
  ## Summary of the ROTS results.
  rots.summary <- summary(rots.out, fdr = 0.05)

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(ROTS)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ROTS/summary.ROTS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: summary.ROTS
> ### Title: Summary of a ROTS object
> ### Aliases: summary.ROTS
> ### Keywords: math
> 
> ### ** Examples
> 
>   ## ROTS-statistic for the Affymetrix spike-in data. 
>   rots.out <- ROTS(data = affySpikeIn, groups = c(rep(0,5), rep(1,5)),
+       B = 100, K = 500 , seed = 1234)
Bootstrapping samples
Optimizing parameters
Calculating p-values
Calculating FDR
>   ## Summary of the ROTS results.
>   rots.summary <- summary(rots.out, fdr = 0.05)
ROTS results: 

Number of resamplings:  100 

a1:                     1.6 
a2:                     1 
Top list size:          10 
Reproducibility value:  0.908 
Z-score:                23.32576 

5 rows satisfy the condition.
         Row ROTS-statistic  pvalue FDR
684_at   315     -4.3078654 0.00002   0
36202_at 555      0.4830924 0.00023   0
36085_at 710      0.4443196 0.00025   0
1024_at  833      0.3993879 0.00027   0
36311_at 303      0.3805451 0.00030   0
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>