Class "aGFFCalc"

Description

Store results of ACME calculations

Objects from the Class

Objects can be created by calls of the form new("aGFFCalc", ...).

Slots

call:

Object of class "call", contains the exact call to do.aGFF.calc, for historical purposes

threshold:

Object of class "numeric", the threshold used in the calculation

cutpoints:

Object of class "numeric", the data value above which probes were considered positive

vals:

Object of class "matrix", equivalent in size to the original data matrix, containing the calculated p-values from the ACME algorithm

annotation:

Object of class "data.frame", currently a copy of the original annotation, possibly reordered in chromosome order

data:

Object of class "matrix", the original data, possibly reordered

samples:

Object of class "data.frame", sample metadata

Extends

Class "aGFF", directly.

Methods

plot

signature(x = "aGFFCalc", ask=FALSE): plot the results of an ACME calculation

print

signature(x = "aGFFCalc"): brief overview of the object

show

signature(object = "aGFFCalc"): brief overview of the object

Author(s)

Sean Davis <sdavis2@mail.nih.gov>

See Also

do.aGFF.calc, aGFF-class

Examples

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data(example.agff)
example.agffcalc <- do.aGFF.calc(example.agff,window=1000,thresh=0.9)
example.agffcalc