summary.ROTS: Summary of a ROTS object

Description

Summarizes the differential testing results from ROTS package.

Usage

"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.

Value

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

Details

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

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

Run this code

  ## 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)

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