summary.ROTS {ROTS} | R Documentation |
Summarizes the differential testing results from ROTS package.
## S3 method for class 'ROTS' summary(object, fdr=NULL, num.genes=NULL, verbose=TRUE, ...)
object |
a |
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. |
This function returns the summary information (including row number, test-statistic, pvalue and FDR value) for the selected features.
Returns a matrix where the rows are the selected features and columns are the Row number, ROTS-statistic, pvalue and FDR.
Fatemeh Seyednasrollah, Tomi Suomi, Laura L. Elo
Maintainer: Fatemeh Seyednasrollah <fatsey@utu.fi>
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.
## 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)