Type: Package
Title: Ordered Panel
Version: 0.1.0
Date: 2026-03-03
Description: The ordered panel methodology (Zezulinski et al 2025 <doi:10.1159/000545366>) provides a structured framework for identifying and organizing sets of biomarkers, such as genetic variants, that distinguish between positive and negative subjects in a study when only a training cohort is available. This approach is particularly useful in situations where an independent validation cohort does not yet exist, rendering conventional performance metrics such as the receiver operating characteristic (ROC) curve and area under the ROC curve (AUC) inappropriate or potentially misleading. The methodology emphasizes transparent construction and evaluation of ordered signatures of biomarkers, allowing investigators to examine operating characteristics without establishing predictive performance.
License: GPL-2
Encoding: UTF-8
Language: en-US
RoxygenNote: 7.3.3
LazyData: true
LazyDataCompression: xz
URL: https://github.com/tingtingzhan/ordPanel, https://tingtingzhan-ordpanel.netlify.app
Depends: R (≥ 4.5.0), flextable, ggplot2
Imports: cli, methods, consort, matrixStats, patchwork, scales
NeedsCompilation: no
Packaged: 2026-03-03 17:09:29 UTC; tingtingzhan
Author: Tingting Zhan ORCID iD [aut, cre], Aejaz Sayeed ORCID iD [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Repository: CRAN
Date/Publication: 2026-03-08 09:50:02 UTC

ordPanel: Ordered Panel

Description

The ordered panel methodology (Zezulinski et al 2025 doi:10.1159/000545366) provides a structured framework for identifying and organizing sets of biomarkers, such as genetic variants, that distinguish between positive and negative subjects in a study when only a training cohort is available. This approach is particularly useful in situations where an independent validation cohort does not yet exist, rendering conventional performance metrics such as the receiver operating characteristic (ROC) curve and area under the ROC curve (AUC) inappropriate or potentially misleading. The methodology emphasizes transparent construction and evaluation of ordered signatures of biomarkers, allowing investigators to examine operating characteristics without establishing predictive performance.

Author(s)

Maintainer: Tingting Zhan tingtingzhan@gmail.com (ORCID)

Other contributors:

See Also

Useful links:

Extract Rows of panel

Description

Extract Rows of panel

Usage

## S3 method for class 'panel'
x[i, ...]

Arguments

x

panel

i

logical vector, row indices

...

additional parameters, currently not in use

Value

The S3 method ⁠[.panel()⁠ returns a panel.

Append to ⁠@label⁠ of panel

Description

Append to ⁠@label⁠ of panel

Usage

append_label(x, info)

Arguments

x

panel

info

character scalar

Value

The function append_label() returns an panel object.

Note

There is no generic function ⁠labels<-⁠ in package base.

The function comment<- is not an S3 generic.

Convert panel into flextable

Description

Convert panel into flextable

Usage

## S3 method for class 'panel'
as_flextable(x, ...)

Arguments

x

panel

...

additional parameters, currently of no use

Value

The S3 method as_flextable.panel() returns a flextable.

Convert a panellist into flextable

Description

Convert a panellist into flextable

Usage

## S3 method for class 'panellist'
as_flextable(x, ...)

Arguments

x

panellist

...

additional parameters, currently of no use

Value

The S3 method as_flextable.panellist() returns a flextable.

Note

The S3 method as_flextable.panellist() may be eventually deprecated.

Visualize panellist using Package ggplot2

Description

Visualize panellist using Package ggplot2

Usage

## S3 method for class 'panellist'
autoplot(object, ...)

## S3 method for class 'panellist'
autolayer(object, which = c("oc", "roc"), ...)

Arguments

object

panellist

...

additional parameters, currently no use

which

character scalar, 'oc' (default value) or (faux) 'roc'

Value

The S3 method autoplot.panellist() returns a ggplot object.

Bibliography in package ordPanel

Description

Bibliography in package ordPanel

Usage

.zezulinski25(key = "Zezulinski25", ...)

Arguments

key, ...

additional parameters of the function bibentry

Value

The function .zezulinski25() returns a bibentry object.

S4 Class panel

Description

S4 Class panel

Usage

panel(m1, m0)

Arguments

m1, m0

see Slots

Value

The function panel() returns an R object of S4 class panel.

Slots

m1

logical matrix, true positives, i.e., variants tested positive in the positive subjects (patients). Rows are different variants. Columns are different subjects. The rownames of m0 and m1 must be the same

m0

logical matrix, false positives, i.e., variants tested positive in the negative subjects (patients). Rows are different variants. Columns are different subjects. The rownames of m0 and m1 must be the same.

id

list of character vectors

label

(optional) character scalar, a human-friendly description of the panel

consort

(optional) data.frame to create a consort_plot

panellist

Description

To combine multiple panels.

Usage

panellist(...)

Arguments

...

one or more panels

Value

The function panellist() returns an S3 object of panellist, which inherits from the classes listof and list.

Data Sets in Package ordPanel

Description

Data sets used as examples in package ordPanel.

Usage

m1

m0

Format

An object of class matrix (inherits from array) with 12877 rows and 50 columns.

An object of class matrix (inherits from array) with 12877 rows and 31 columns.

References

doi:10.1159/000545366

Examples

# data used in 
.zezulinski25()

CONSORT-Like Flow-Chart of Ordered panel

Description

To create a CONSORT-Like flow-chart of an ordered panel.

Usage

## S3 method for class 'panel'
plot(x, ...)

Arguments

x

an ordered panel

...

additional parameters of the function consort_plot, except for data, orders and side_box

Value

The function plot.panel() returns an R object of class 'consort'.

CONSORT-Like Flow-Chart of Ordered panellist

Description

To create a CONSORT-Like flow-chart of an ordered panellist.

Usage

## S3 method for class 'panellist'
plot(x, ...)

Arguments

x

an ordered panellist

...

additional parameters for the function wrap_plots, not for the function plot.panel()

Value

The function plot.panellist() returns a patchwork.

Show panel

Description

Show panel

Usage

## S4 method for signature 'panel'
show(object)

Arguments

object

panel

Value

The show method of panel class does not have a returned value.l

Sort panel by Given Criterion

Description

Sort panel by Given Criterion

Usage

## S3 method for class 'panel'
sort_by(x, y, ...)

Arguments

x

panel

y

one-sided formula

...

additional parameters of order

Value

The S3 method sort_by.panel() returns a panel.

Select a subset of panel

Description

Select a subset of panel

Usage

## S3 method for class 'panel'
subset(x, subset, append.label = FALSE, ...)

Arguments

x

panel

subset

R language object

append.label

logical scalar (default value FALSE), whether to append the subset-criterion to x@label

...

additional parameters, currently not in use

Value

The S3 method subset.panel() returns an R object of S4 class panel.

Number of True & False Positives, per variant

Description

Number of True & False Positives, per variant

Usage

sum1(x)

sum0(x)

cumsum1(x)

cumsum0(x)

Arguments

x

panel

Value

The functions sum1() and sum0() return a integer vector.

The functions cumsum1() and cumsum0() return a strictly increasing integer vector.