ROC {cellHTS2} | R Documentation |
The function ROC
construct an object of S4 class ROC
,
which represents a receiver-operator-characteristic curve,
from the data of the annotated positive and negative controls in a
scored cellHTS
object.
## S4 method for signature 'cellHTS': ROC(object, positives, negatives) ## S4 method for signature 'ROC, missing': plot(x, col="darkblue", type="l", main = "ROC curve", ...) ## S4 method for signature 'ROC': lines(x, ...)
object |
a cellHTS object which replicate data have already been scored and summarized (see details). |
positives |
a list or vector of regular expressions specifying the name of the positive control(s).
See the details for the argument posControls of writeReport function. The default is "^pos$" . |
negatives |
a vector of regular expressions specifying the name of the negative control(s).
See the details for the argument negControls of writeReport function. The default is "^neg$" . |
x |
a ROC object obtained using function ROC . |
col |
the graphical parameter for color; see par for details. |
type |
the graphical parameter giving the type of plot desired; see par for details. |
main |
the graphical parameter giving the desired title of plot; see par for details. |
... |
other graphical parameters as in par may be also passed as arguments. |
The cellHTS
object object
must be already scored (state(object)["scored"]=TRUE
),
and selection proceeds from large to small values of this single per-probe score.
Furthermore, object
is expected to contain positive and negative
controls annotated in the column controlStatus
of the featureData
slot - which can be accessed via wellAnno(object)
. The arguments positives
and negatives
should be given as regular expression patterns specifying the name of the positive(s) and negative(s) controls, respectivey.
By default, if positives
is not given, pos will be taken as the name for the wells containing positive controls. Similarly, if negatives
is missing, by default neg will be considered as the name used to annotate the negative controls.
The content of posControls
and negControls
are passed to regexpr
for pattern matching within the well annotation (see examples for summarizeChannels
).
If the assay is a two-way experiment, positives
should be a list with components act
and inh
, specifying the name of the activators, and inhibitors, respectively. In this case, the ROC curve is constructed based on the absolute values of Data(object)
.
An S4 object of class ROC
. There are methods show
,
plot
and lines
.
Ligia P. Bras ligia@ebi.ac.uk
data(KcViabSmall) x <- normalizePlates(KcViabSmall, scale="multiplicative", log=FALSE, method="median", varianceAdjust="byExperiment") x <- scoreReplicates(x, sign="-", method="zscore") x <- summarizeReplicates(x, summary="mean") y <- ROC(x) plot(y) lines(y, col="green") show(y)