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ACME (version 2.28.0)

aGFFCalc-class: Class "aGFFCalc"

Description

Store results of ACME calculations

Arguments

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

See Also

do.aGFF.calc, aGFF-class

Examples

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

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