R: SAM specific summary method

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

`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