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</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 <delta> 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`