sumSAM-class: 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.