summary.ROTS: Summary of a ROTS object

In ROTS: Reproducibility-Optimized Test Statistic

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: Tomi Suomi <[e-mail]>

References

Suomi T, Seyednasrollah F, Jaakkola MK, Faux T, Elo LL.
ROTS: An R package for reproducibility-optimized statistical testing.
PLoS Comput Biol 2017; 13: e1005562.

See Also

affySpikeIn

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)

Example output

Bootstrapping samples
Optimizing parameters
Calculating p-values
Calculating FDR
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

ROTS documentation built on Nov. 8, 2020, 7:37 p.m.