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

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