summary.ROTS {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: Tomi Suomi <tomi.suomi@utu.fi>

### 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)

[Package ROTS version 1.20.0 Index]