summary {siggenes}R Documentation

SAM specific summary method

Description

Summarizes a SAM analysis. Computes either general statistics as the number of differentially expressed genes and the estimated FDR for a vector of Delta values or gene-specific statistics for the differentially expressed genes when just one Delta value is specified

Usage

summary(object, delta = NULL, n.digits = 5, what = "both", entrez = FALSE, bonf = FALSE,
	chip = "", file = "", sep = "\t", quote = FALSE, dec=".")

Arguments

object a SAM object
delta a numeric value or vector specifying one or a set of Deltas. If NULL or a vector general statistics as the number of differentially expressed genes and the estimated FDR will be computed. If delta is a value not only the above statistics will be computed but also gene-specific information on the differentially expressed genes will be given -- see what
n.digits an integer specifying the number of decimal places in the output
what either "both", "stats" or "genes". If "stats" general information is shown. If "genes" gene-specific information is given. If "both" both general and gene-specific information is shown. Will be ignored if delta is NULL or a vector
entrez logical. If TRUE both the Entrez links and the symbols of the genes will be added to the output
bonf logical. If TRUE Bonferroni corrected p-values will be added to the output
chip character string naming the chip type used in this analysis. Only needed if entrez = TRUE. If the argument data of sam(data,cl,...) has been specified by an ExpressionSet object chip need not to be specified
file character string naming the file in which the information should be stored. By default the information is not stored but shown in the R window. Will be ignored if delta is NULL or a vector
sep the field separator string used when output is stored in file
quote logical indicating if character strings and factors should be surrounded by double quotes. For details see ?write.table
dec the string to use for decimal points

Value

The output of summary consists of the following slots:
row.sig.genes a numeric vector specifying the rows of the data matrix containing the differentially expressed genes. If is NULL or a vector, row.sig.genes> will be numeric(0)
mat.fdr a numeric vector (if delta is a numeric value) or a matrix containing general information as the estimated FDR and the number of differentially expressed genes
mat.sig a data frame containing gene-specific information on the differentially expressed genes
list.args a list containing the arguments of summary needed for internal use

Note

SAM was deveoped by Tusher et al. (2001).

!!! There is a patent pending for the SAM technology at Stanford University. !!!

Author(s)

Holger Schwender, holger.schw@gmx.de

References

Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. PNAS, 98, 5116-5121.

See Also

sam, SAM-class, print, sam2excel, sam2html