aGFFCalc-class: Class "aGFFCalc"

Description Objects from the Class Slots Extends Methods Author(s) See Also Examples

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


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