The "QcMetrics" class for collections of QC items

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

Laurent Gatto

See also

The QcMetric class for individual QC items.

Examples

example(QcMetric)
#> 
#> QcMtrc> (qc <- QcMetric())
#> Object of class "QcMetric"
#>  Name: A QcMetric prototype 
#>  Status: NA 
#>  Data: empty
#> 
#> QcMtrc> qcdata(qc)
#> character(0)
#> 
#> QcMtrc> try(qcdata(qc, "x"))
#> Error in qcdata(qc, "x") : No qcdata 'x' in object.
#> 
#> QcMtrc> x <- rnorm(10)
#> 
#> QcMtrc> qcdata(qc, "qc1") <- x
#> 
#> QcMtrc> qcdata(qc, "qc2") <- 1:10
#> 
#> QcMtrc> qcdata(qc)
#> [1] "qc1" "qc2"
#> 
#> QcMtrc> all.equal(qcdata(qc, "qc1"), x)
#> [1] TRUE
#> 
#> QcMtrc> all.equal(qcdata(qc, "qc2"), 1:10)
#> [1] TRUE
#> 
#> QcMtrc> name(qc) <- "My test QcMetric"
#> 
#> QcMtrc> description(qc) <- "This qc metric describes bla bla bla, indicating possible issues in the third step of protocol bla bla bla."
#> 
#> QcMtrc> status(qc) <- FALSE
#> 
#> QcMtrc> qc
#> Object of class "QcMetric"
#>  Name: My test QcMetric 
#>  Description:
#> This qc metric describes bla bla bla, indicating possible issues in the
#> third step of protocol bla bla bla.
#>  Status: FALSE 
#>  Data: qc1 qc2 
#> 
#> QcMtrc> ## or
#> QcMtrc> e <- new.env()
#> 
#> QcMtrc> e$qc1 <- rnorm(100)
#> 
#> QcMtrc> e$qc2 <- 1:100
#> 
#> QcMtrc> qcenv(qc) <- e
#> 
#> QcMtrc> length(qcdata(qc, "qc1"))
#> [1] 100
#> 
#> QcMtrc> head(qcdata(qc, "qc2"))
#> [1] 1 2 3 4 5 6
#> 
#> QcMtrc> show(qc)
#> Object of class "QcMetric"
#>  Name: My test QcMetric 
#>  Description:
#> This qc metric describes bla bla bla, indicating possible issues in the
#> third step of protocol bla bla bla.
#>  Status: FALSE 
#>  Data: qc1 qc2 
#> 
#> QcMtrc> show(qc) <- function(object) cat("Updated show method\n")
#> 
#> QcMtrc> show(qc)
#> Updated show method
#> 
#> QcMtrc> show(qc) <- qcshow
#> 
#> QcMtrc> qc
#> Object of class "QcMetric"
#>  Name: My test QcMetric 
#>  Description:
#> This qc metric describes bla bla bla, indicating possible issues in the
#> third step of protocol bla bla bla.
#>  Status: FALSE 
#>  Data: qc1 qc2 
#> 
#> QcMtrc> plot(qc)
#> Warning: No specific plot function defined
#> 
#> QcMtrc> plot(qc) <-
#> QcMtrc+     function(object, ...)
#> QcMtrc+         plot(qcdata(object, "qc2"),
#> QcMtrc+              qcdata(object, "qc1"),
#> QcMtrc+              xlab = "qc1",
#> QcMtrc+              ylab = "qc2",
#> QcMtrc+              ...)
#> 
#> QcMtrc> plot(qc)

#> 
#> QcMtrc> plot(qc, col = "red", pch = 19)

show(qc)
#> Object of class "QcMetric"
#>  Name: My test QcMetric 
#>  Description:
#> This qc metric describes bla bla bla, indicating possible issues in the
#> third step of protocol bla bla bla.
#>  Status: FALSE 
#>  Data: qc1 qc2 

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
#> Object of class "QcMetrics"
#>  containing 2 QC metrics.
#>  and no metadata variables.

qcm[1] ## a QcMetrics instance
#> Object of class "QcMetrics"
#>  containing 1 QC metrics.
#>  and no metadata variables.
qcm[[1]] ## a single QcMetric
#> Object of class "QcMetric"
#>  Name: My test QcMetric 
#>  Description:
#> This qc metric describes bla bla bla, indicating possible issues in the
#> third step of protocol bla bla bla.
#>  Status: FALSE 
#>  Data: qc1 qc2 

metadata(qcm)
#> list()
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)
#> $name
#> [1] "Prof. Who"
#> 
#> $lab
#> [1] "Cabin University"
#> 
## update metadata
metadata(qcm) <- list(lab = "Big lab", ## updated
                      uni = "Cabin University") ## added
mdata(qcm)
#> $name
#> [1] "Prof. Who"
#> 
#> $lab
#> [1] "Big lab"
#> 
#> $uni
#> [1] "Cabin University"
#>