GEVAQuantiles-class {geva} | R Documentation |
The GEVAQuantiles
class represents the results of a quantile detection analysis. For each probe/gene, there is a assigned quantile among the g defined quantiles.
This class inherits from GEVAGroupSet
and is inherited by GEVAQuantilesAdjusted
.
A GEVAQuantiles
object
grouping
factor
(m elements, g levels), quantile assignment for each gene/probe
(Inherited from GEVAGroupSet
)
scores
numeric
vector (m elements) with the assigned quantile scores for each gene/probe
(Inherited from GEVAGroupSet
)
ftable
data.frame
(m lines) with additional quantile assignment features
(Inherited from GEVAGroupSet
)
centroids
numeric SVTable
(g lines) with the S and V centroid coordinates for each quantile
(Inherited from GEVAGroupSet
)
offsets
numeric SVTable
(m lines) with the S and V coordinate offsets each gene/probe from its quantile centroid
(Inherited from GEVAGroupSet
)
info
list
of additional information
(Inherited from GEVAGroupSet
)
svscores
numeric SVTable
(m lines) with individual partial scores for the assigned quantiles
qareasizes
numeric SVTable
(g lines) with the S and V sizes for each quantile
qindexes
integer SVTable
(g lines) representing the position index to each quantile, in terms of summary and variation
qcount
integer attributes (SVIntAttribute
) with the defined number of quantiles for the S and V axes
qcutoff
numeric attributes (SVNumAttribute
) with the initial quantile cutoff in S and V, starting from the point zero
qmethod
character
, method used to calculate the initial quantiles (see geva.quantiles()
)
(See also the inherited methods from GEVAGroupSet
)
Conversion and coercion
as.expression(x, sv, ...)
Converts this object to expression
as.SVTable(
x,
which = c("sv", "offsets", "centroids", "qindexes"),
...,
row.names = names(x)
)
Converts this object to SVTable
Plotting
lines(x, ...)
Draws the quantile delimiter lines
plot(x, y, ...)
Draws a SV-plot that highlights the points from each quantile. Dashed lines are included as the quantile delimiters.
Can be combined with another SVTable
or GEVAGroupSet
given as the y
argument to include additional graphical elements
Properties
cluster.method(object)
Returns the option used as the cluster.method
argument when calling geva.cluster
.
Instances of this object always return 'quantiles'
Sub-slot accessors
classification.table(object) <- value
Sets the data.frame
with the qualitative contrasts of classification relevance
classification.table(object)
Gets a data.frame
with the qualitative contrasts of classification relevance
quantiles(object)
Gets the unique quantile names