sumSAM-class {siggenes} | R Documentation

## Classes sumSAM and sumEBAM

### Description

These classes are just used for a nicer output of the summary of an object of class SAM or EBAM, respectively.

### Objects from the Class

Objects can be created by calls of the form `new("sumSAM", ...)`, or by using the function `summary(object)` when object is a SAM-class object.

Objects can be created by calls of the form `new("sumEBAM", ...)`, or by using the function `summary(object)` when object is an EBAM-class object.

### Slots

`row.sig.genes`:

  Object of class `"numeric"` consisting of the row numbers of the significant genes in the data matrix.

`mat.fdr`:

  Object of class `"matrix"` containing general information as the number of differentially expressed genes and the estimated FDR for either one or several values of Delta.

`mat.sig`:

  Object of class `"data.frame"` containing gene-specific statistics as the d-values (or z-values) and the q-values or (the local FDR) of the differentially expressed genes.

`list.args`:

  Object of class `"list"` consisting of some of the specified arguments of summary needed for internal use.

### Methods

print

  `signature(x = "sumSAM")`: Prints the output of the SAM-specific method summary.

show

  `signature(object = "sumSAM")`: Shows the output of the summary of a SAM analysis.

print

  `signature(x = "sumEBAM")`: Prints the output of the EBAM-specific method summary.

show

  `signature(object = "sumEBAM")`: Shows the output of the summary of a EBAM analysis.

### Author(s)

Holger Schwender, holger.schw@gmx.de

### See Also

`SAM-class`, `EBAM-class`

[Package siggenes version 1.58.0 Index]