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 1.18.0 Index]