QcMetrics-class: The '"QcMetrics"' class for collections of QC items
In lgatto/qcmetrics: A Framework for Quality Control

QcMetrics-class

R Documentation

The `"QcMetrics"` class for collections of QC items

Description

Data structure for storing lists of QcMetric items.

Objects from the Class

Objects can be created using the constructor QcMetrics(...), where slots are assigned individually. See example below.

In a standardised quality control pipeline, the QcMetrics and QcMetric object are not generated manually. Their creation is delegated to a wrapper function that reads a specific type of files, parses the data, produces the individual QcMetric instances and, eventually, the QcMetric object. See the package vignette for details and examples.

Slots

metadata:: Object of class QcMetadata storing the metadata of the object. This list would typically contain the input file the data was read from, the date the object was generated, ... or fully fledged minimum information descriptions (see MIAxE), when available.
qcdata:: Object of class "list" storing all the individual QcMetric instances.

Methods

[: signature(x = "QcMetrics"): subsets x as a new QcMetrics instance.
[[: signature(x = "QcMetrics"): extracts a single QcMetric instance.
length: signature(x = "QcMetrics"): returns the number of QcMetric instances populate x.
metadata: signature(x = "QcMetrics"): return the object's metadata list. Also available as mdata.
metadata<-: signature(x = "QcMetrics", value = "list"): sets the objects metadata. Also available as mdata.
metadata<-: signature(x = "QcMetric", value = "QcMetadata"): sets the objects metadata. Also available as mdata.
name: signature(object = "QcMetrics"): returns a character vector of length length(object) with the names of the QcMetric instances.
qcdata: signature(object = "QcMetrics", x = "missing"): returns a list of all QcMetric instances.
qcdata<-: signature(object = "QcMetrics", value = "list"): sets the qcdata of object.
show: signature(object = "QcMetrics"): prints a short textual description of object.
status: signature(object = "QcMetrics"): returns a vector of quality statuses (logicals).
status<-: signature(object = "QcMetrics", value = "logical"): sets the quality statuses. Length of value and object must be identical.
as: signature(object = "QcMetrics", "data.frame"): coerces object as a length(object) by 2 data frame with the respective QcMetric instances names and statuses.
qcReport: signature(object = "QcMetrics"): ...

Author(s)

Laurent Gatto

Examples

example(QcMetric)
show(qc)

qc2 <- QcMetric(name = "My other metric", status = TRUE)
qcdata(qc2, "x") <- rnorm(100)
qcdata(qc2, "k") <- rep(LETTERS[1:2], 50)

plot(qc2) <- function(object, ...) {
    require("lattice")
    d <- data.frame(x = qcdata(object, "x"),
                    k = qcdata(object, "k"))
    bwplot(x ~ k, data = d)
}

qcm <- QcMetrics(qcdata = list(qc, qc2))
qcm

qcm[1] ## a QcMetrics instance
qcm[[1]] ## a single QcMetric

metadata(qcm)
metadata(qcm) <- QcMetadata(list(name = "Prof. Who",
                                 lab = "Cabin University"))
## or, shorter but equivalent
metadata(qcm) <- list(name = "Prof. Who",
                      lab = "Cabin University")
metadata(qcm) ## or mdata(qcm)
## update metadata
metadata(qcm) <- list(lab = "Big lab", ## updated
                      uni = "Cabin University") ## added
mdata(qcm)

lgatto/qcmetrics documentation built on Feb. 4, 2024, 12:20 p.m.