summary.ACE {ADaCGH} | R Documentation |
Shows the number of genes detected as gains/loss at different levels of FDR, allows setting the desired FDR, and returns the assigned status of each genes for the selected FDR.
## S3 method for class 'ACE': summary(object, fdr = NULL, html = TRUE, outhtml = "ace.fdrtable.html", ...)
object |
An object of class ACE or ACE.array, as returned from pSegmentACE |
fdr |
The desired FDR. The actual value used is the closest one the desired. If NULL, the FDR selected is the closest one to 0.15. |
html |
If TRUE, produce also an HTML table |
outhtml |
The name of the file with the HTML output |
... |
Not used. |
Calling this function always returns (prints) a table with the number of Genes called gains/losses at each of the available FDRs and the index (row) corresponding to the selected FDR (or the closest FDR to 0.15). Additionally, a list with as many components as samples. Each list component is a data frame with genes/clones as rows and three columns: the chromosome identifier, the original log-ratio, and the status (0 for no change, -1 for loss, +1 for gain).
Oscar M. Rueda omrueda@cnio.es
Lingjaerde OC, Baumbusch LO, Liestol K, Glad I, Borresen-Dale AL. (2005). CGH-Explorer: a program for analysis of CGH-data. Bioinformatics, 21: 821–822.
Diaz-Uriarte, R. and Rueda, O.M. (2006). ADaCGH: an R package and web-based application for the analysis of aCGH data. Tech. report. http://www.ligarto.org/rdiaz/Papers/adacgh.pdf, http://adacgh.bioinfo.cnio.es.
## Not run: data(cghMCRe) chrom.numeric <- as.numeric(as.character(cghMCRe$Chromosome)) chrom.numeric[cghMCRe$Chromosome == "X"] <- 23 chrom.numeric[cghMCRe$Chromosome == "Y"] <- 24 ## Recall: we must reorder the data by chromosome and ## by position within chromosome reorder <- order(chrom.numeric, cghMCRe$Start, cghMCRe$End, cghMCRe$Name) cghMCRe <- cghMCRe[reorder, ] chrom.numeric <- chrom.numeric[reorder] ace.out <- pSegmentACE(cghMCRe[, 5:7], chrom.numeric) summary(ace.out, fdr = 0.01) ## End(Not run)