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summary.ACE {ADaCGH}

Gains/loss and FDR from an ACE object
Package: 
ADaCGH
Version: 
1.5-3

Description

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.

Usage

 
## S3 method for class 'ACE':
summary((object, fdr = NULL, html = TRUE,
            outhtml = "ace.fdrtable.html", ...))

Arguments

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.

Values

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).

References

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.

See Also

pSegmentACE, segmentPlot

Examples

## 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)

Author(s)

Oscar M. Rueda omrueda@cnio.es

Documentation reproduced from package ADaCGH, version 1.5-3. License: GPL (>= 3)