| Type: | Package |
| Title: | Pharmacokinetic Bioanalysis Experiments Design and Exploration |
| Version: | 0.3.0 |
| Maintainer: | Omar Elashkar <omar.i.elashkar@gmail.com> |
| Description: | Automate pharmacokinetic/pharmacodynamic bioanalytical procedures based on best practices and regulatory recommendations. The package impose regulatory constrains and sanity checking for common bioanalytical procedures. Additionally, 'PKbioanalysis' provides a relational infrastructure for plate management and injection sequence. |
| License: | AGPL (≥ 3) |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| Depends: | R (≥ 4.3.0) |
| Imports: | dplyr (≥ 1.1.3), tidyselect, stringr (≥ 1.5.1), ggplot2 (≥ 3.5.1), ggforce (≥ 0.4.1), tidyr (≥ 1.3.0), glue (≥ 1.6.2), checkmate, shiny (≥ 1.9.1), DBI, duckdb (≥ 1.0.0), bslib, bsicons, shinyWidgets, shinyjs, DiagrammeR, units, DT, stats, shinyalert, htmltools, rlang, grDevices, utils, yaml, rhandsontable, methods |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0) |
| URL: | https://omarashkar.github.io/PKbioanalysis/ |
| BugReports: | https://github.com/OmarAshkar/PKbioanalysis/issues |
| Config/testthat/edition: | 3 |
| NeedsCompilation: | no |
| Packaged: | 2025-05-21 17:30:50 UTC; omar.elashkar |
| Author: | Omar Elashkar 
[aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2025-05-21 17:50:01 UTC |
PKbioanalysis: Pharmacokinetic Bioanalysis Experiments Design and Exploration
Description
Automate pharmacokinetic/pharmacodynamic bioanalytical procedures based on best practices and regulatory recommendations. The package impose regulatory constrains and sanity checking for common bioanalytical procedures. Additionally, 'PKbioanalysis' provides a relational infrastructure for plate management and injection sequence.
Author(s)
Maintainer: Omar Elashkar omar.i.elashkar@gmail.com (ORCID)
See Also
Useful links:
Report bugs at https://github.com/OmarAshkar/PKbioanalysis/issues
Subsetting method for MultiPlate
Description
Subsetting method for MultiPlate
Usage
## S4 method for signature 'MultiPlate'
x[[i, j, ...]]
Arguments
x |
MultiPlate object |
i |
index |
j |
index |
... |
additional arguments |
Value
PlateObj object
Add double blank (DB) to a plate
Description
Add double blank (DB) to a plate
Usage
add_DB(plate)
Arguments
plate |
PlateObj object |
Value
PlateObj
Examples
plate <- generate_96() |>
add_DB()
Add dilution quality control (DQC) to the plate
Description
Add dilution quality control (DQC) to the plate
Usage
add_DQC(plate, conc, fac, rep = 5)
Arguments
plate |
PlateObj object |
conc |
numeric. Concentration of the DQC well. |
fac |
numeric. Factor of the DQC well. |
rep |
numeric. Number of replicates. Default is 5. The current implementation does not check ULOQ or LLOQ boundaries. |
Add quality control samples to the plate
Description
A function to add QCs to plate. This function assumes adherence to ICH guideline M10 on bioanalytical method validation and study sample analysis Geneva, Switzerland (2022). If you are not following this guideline, you can set 'reg = TRUE' to ignore the restrictions.
Usage
add_QC(
plate,
lqc_conc,
mqc_conc,
hqc_conc,
extra = NULL,
n_qc = 3,
qc_serial = TRUE,
reg = TRUE
)
Arguments
plate |
PlateObj object |
lqc_conc |
low quality control concentration |
mqc_conc |
medium quality control concentration |
hqc_conc |
high quality control concentration |
extra |
numeric vector of extra QC concentrations. Default is NULL. |
n_qc |
number of QC sets. Default is 3 |
qc_serial |
logical. If TRUE, QCs are placed serially |
reg |
logical. Indicates if restrictions should not be applied to the QC samples. Default is TRUE |
Value
PlateObj
Add blank to the plate Can be either double blank (DB), CS0IS+ or CS1IS-
Description
Add blank to the plate Can be either double blank (DB), CS0IS+ or CS1IS-
Usage
add_blank(plate, IS = TRUE, analyte = FALSE)
Arguments
plate |
PlateObj object |
IS |
logical. If TRUE, add IS to the well. |
analyte |
logical. If TRUE, add analyte to the well. |
Value
PlateObj
Add calibration curve to the plate
Description
Add calibration curve to the plate
Usage
add_cs_curve(plate, plate_std, rep = 1)
Arguments
plate |
PlateObj |
plate_std |
character |
rep |
numeric. Number of replicates. Default is 1. |
Value
PlateObj
Examples
plate <- generate_96() |>
add_cs_curve(c(1, 3, 5, 10, 50, 100, 200))
plot(plate)
Add unknown samples to a plate
Description
Add unknown samples to a plate
Usage
add_samples(
plate,
samples,
time = NA,
conc = NA,
dil = NA,
factor = NA,
dosage = NA,
prefix = "S",
vtime = FALSE
)
Arguments
plate |
PlateObj |
samples |
A vector representing samples names. Must be unique. |
time |
A vector representing time points. If vtime = FALSE, time will propagate to all samples. |
conc |
A vector representing concentration. Must be same length as samples. |
dil |
A vector representing dilution factor. Must be same length as samples. |
factor |
A vector representing factor. Must be same length as samples. |
dosage |
A vector representing dosage. Must be same length as samples. |
prefix |
A prefix to be added before samples names. Default is "S" |
vtime |
A logical. If TRUE, time is a vector of sample length as samples. Default is FALSE. |
Details
final name will be of form. Prefix-SampleName-Time-Concentration-Factor samples must be a unique vector and did not exist in the plate before. Time is either a vector or a single value. If it is a vector, it will be repeated for each sample. Conc, dil, factor and dosage are either a vector or a single value. If it is a vector, it must be the corrosponding length of samples.
Value
PlateObj
Examples
plate <- generate_96() |>
add_samples(paste0("T", 1:12))
Cartesian product of sample factors to a plate
Description
Cartesian product of sample factors to a plate
Usage
add_samples_c(
plate,
n_rep,
time = NA,
conc = NA,
factor = NA,
dosage = NA,
prefix = "S"
)
Arguments
plate |
PlateObj |
n_rep |
number of samples to be added |
time |
A vector representing time points |
conc |
A vector representing concentration |
factor |
A vector representing factor |
dosage |
A vector representing dosage |
prefix |
A prefix to be added before samples names. Default is "S" |
Details
This function is a variation of 'add_samples()' where size of inputs does not matter. The function will automatically create a combination of all sample names with time, concentration and factor. final name will be of form. Prefix-SampleName-Time-Concentration-Factor
Value
PlateObj
Add suitability sample to the plate
Description
Add suitability sample to the plate
Usage
add_suitability(plate, conc, label = "suitability")
Arguments
plate |
PlateObj object. |
conc |
numeric. Concentration of the suitability well. |
label |
character. Label for the suitability well. Default is "suitability". |
Value
PlateObj
Create Injection Sequence
Description
Create Injection Sequence
Usage
build_injec_seq(
plate,
method,
repeat_std = 1,
repeat_qc = 1,
repeat_analyte = 1,
blank_after_top_conc = TRUE,
blank_at_end = TRUE,
system_suitability = 0,
blank_every_n = NULL,
inject_vol,
descr = "",
prefix = Sys.Date(),
suffix = "1",
tray = 1,
explore_mode = FALSE,
conc_df = NULL
)
Arguments
plate |
PlateObj object |
method |
choose method from database |
repeat_std |
number of re-injections for calibration standards. Default is 1. |
repeat_qc |
number of re-injections for QC wells. Default is 1 |
repeat_analyte |
number of re-injections for unknown samples. Default is 1 |
blank_after_top_conc |
If TRUE, adding blank after high concentrations of standards and QCS. |
blank_at_end |
If True, adding blank at the end of queue. |
system_suitability |
Number of re-injections for suitability vial. |
blank_every_n |
If no QCs, frequency of injecting blanks between analytes. |
inject_vol |
volume of injection in micro liters. |
descr |
Run description. |
prefix |
string at the beginning of the filename. Default is today's date. |
suffix |
string to be added to the end of the filename. Default is "1". |
tray |
Location in sample manager. |
explore_mode |
options either TRUE or FALSE. Default if FALSE. |
conc_df |
data.frame matching compound name to a scaling factor. Maximum 20 compounds allowed. |
Details
explore_mode controls if exploratory samples are to be injected. A random sample from each CS and QC group will be sampled along with 1 blank sample.
Value
InjecListObj object
Create Injection Sequence from MultiPlate (Multiple Plates)
Description
Create Injection Sequence from MultiPlate (Multiple Plates)
Usage
## S4 method for signature 'MultiPlate'
build_injec_seq(
plate,
method,
repeat_std = 1,
repeat_qc = 1,
repeat_analyte = 1,
blank_after_top_conc = TRUE,
blank_at_end = TRUE,
system_suitability = 0,
blank_every_n = NULL,
inject_vol,
descr = "",
prefix = Sys.Date(),
suffix = "1",
tray = 1,
explore_mode = FALSE,
conc_df = NULL
)
Arguments
plate |
MultiPlate object |
method |
choose method from database |
repeat_std |
number of re-injections for calibration standards. Default is 1. |
repeat_qc |
number of re-injections for QC wells. Default is 1 |
repeat_analyte |
number of re-injections for unknown samples. Default is 1 |
blank_after_top_conc |
If TRUE, adding blank after high concentrations of standards and QCS. |
blank_at_end |
If True, adding blank at the end of queue. |
system_suitability |
Number of re-injections for suitability vial. |
blank_every_n |
If no QCs, frequency of injecting blanks between analytes. |
inject_vol |
volume of injection in micro liters. |
descr |
Run description. |
prefix |
string at the beginning of the filename. Default is today's date. |
suffix |
string to be added to the end of the filename. Default is "1". |
tray |
Location in sample manager. |
explore_mode |
options either TRUE or FALSE. Default if FALSE. |
conc_df |
data.frame matching compound name to a scaling factor. Maximum 20 compounds allowed. |
Value
InjecListObj object
Create Injection Sequence from PlateObj (Single Plate)
Description
Create Injection Sequence from PlateObj (Single Plate)
Usage
## S4 method for signature 'PlateObj'
build_injec_seq(
plate,
method,
repeat_std = 1,
repeat_qc = 1,
repeat_analyte = 1,
blank_after_top_conc = TRUE,
blank_at_end = TRUE,
system_suitability = 0,
blank_every_n = NULL,
inject_vol,
descr = "",
prefix = Sys.Date(),
suffix = "1",
tray = 1,
explore_mode = FALSE,
conc_df = NULL
)
Arguments
plate |
PlateObj object |
method |
choose method from database |
repeat_std |
number of re-injections for calibration standards. Default is 1. |
repeat_qc |
number of re-injections for QC wells. Default is 1 |
repeat_analyte |
number of re-injections for unknown samples. Default is 1 |
blank_after_top_conc |
If TRUE, adding blank after high concentrations of standards and QCS. |
blank_at_end |
If True, adding blank at the end of queue. |
system_suitability |
Number of re-injections for suitability vial. |
blank_every_n |
If no QCs, frequency of injecting blanks between analytes. |
inject_vol |
volume of injection in micro liters. |
descr |
Run description. |
prefix |
string at the beginning of the filename. Default is today's date. |
suffix |
string to be added to the end of the filename. Default is "1". |
tray |
Location in sample manager. |
explore_mode |
options either TRUE or FALSE. Default if FALSE. |
conc_df |
data.frame matching compound name to a scaling factor. Maximum 20 compounds allowed. |
Value
InjecListObj object
Create Sample List with rigorous design
Description
Create Sample List with rigorous design
Usage
combine_injec_lists(
sample_lists,
n_equi = 10,
equi_pos,
equi_prefix = Sys.Date(),
equi_suffix = "equi",
equi_injec_vol = 0.5
)
Arguments
sample_lists |
a list of sample lists |
n_equi |
number of equilibriation injections |
equi_pos |
position of equilibriation injections. For format check details |
equi_prefix |
prefix for equilibriation injections |
equi_suffix |
suffix for equilibriation injections |
equi_injec_vol |
volume of equilibriation injection |
Details
The equi_pos format will be Row:Column format. E.g: "A,1"
Value
InjecListObj object
Combine plates in MultiPlate object
Description
Combine plates in MultiPlate object
Usage
combine_plates(plates)
Arguments
plates |
list of PlateObj objects |
Value
MultiPlate object
Download sample list from database to local spreadsheet with vendor specific format
Description
Download sample list from database to local spreadsheet with vendor specific format
Usage
download_sample_list(sample_list, vendor)
Arguments
sample_list |
dataframe of sample list either from db or from write_injec_seq |
vendor |
currently only 'masslynx', 'masshunter' and 'analyst' are supported |
Details
For all current vendors, the exported format will be in csv format, compatible with the respective software.
Value
dataframe
Filling orientation of the plate
Description
This function sets the filling scheme of the plate. The filling scheme is used to determine the order in which the samples are filled in the plate. The default filling scheme is horizontal, which means that the samples are filled from left to right and top to bottom. The vertical filling scheme means that the samples are filled from top to bottom and left to right.
Usage
fill_scheme(
plate,
fill = "h",
tbound = "A",
bbound = "H",
lbound = 1,
rbound = 12
)
Arguments
plate |
PlateObj |
fill |
character. Filling scheme. Either "h" for horizontal, "v" for vertical. |
tbound |
character. Top bound of the filling scheme. Default is "A" |
bbound |
character. Bottom bound of the filling scheme. Default is "H" |
lbound |
numeric. Left bound of the filling scheme. Default is 1 |
rbound |
numeric. Right bound of the filling scheme. Default is 12 |
Value
PlateObj
Generate 96 Plate Generate a typical 96 well plate. User need to specify the empty rows which a going to be used across the experiment.
Description
Generate 96 Plate Generate a typical 96 well plate. User need to specify the empty rows which a going to be used across the experiment.
Usage
generate_96(descr = "", start_row = "A", start_col = 1)
Arguments
descr |
plate description. |
start_row |
A letter corresponding to empty rows in a 96 well plate. Default is A. |
start_col |
A number indicating a column number to start with, given the start row. Default is 1. |
Value
PlateObj
Examples
plate <- generate_96()
plot(plate)
plate <- generate_96("calibration", start_row = "C", start_col = 11)
plot(plate)
Length method for MultiPlate
Description
Length method for MultiPlate
Usage
## S4 method for signature 'MultiPlate'
length(x)
Arguments
x |
MultiPlate object |
Value
number of plates
Create a calibration study with calibration standards and QCs
Description
Create a calibration study with calibration standards and QCs
Usage
make_calibration_study(
plate,
plate_std,
lqc_conc = NULL,
mqc_conc = NULL,
hqc_conc = NULL,
n_qc = NULL,
qc_serial = FALSE,
n_CS0IS0 = 1,
n_CS0IS1 = 2,
n_CS1IS0 = 1
)
Arguments
plate |
PlateObj object |
plate_std |
vector of calibration standards |
lqc_conc |
LQC concentration |
mqc_conc |
MQC concentration |
hqc_conc |
HQC concentration |
n_qc |
number of QC sets |
qc_serial |
logical. If TRUE, QCs are placed serially |
n_CS0IS0 |
number of CS0IS0 (double) blanks |
n_CS0IS1 |
number of CS0IS1 blanks |
n_CS1IS0 |
number of CS1IS0 blanks |
Value
PlateObj
Create a metabolic study layout
Description
Create a metabolic study layout
Usage
make_metabolic_study(
cmpds,
time_points = c(0, 5, 10, 15, 30, 45, 60, 75, 90, 120),
n_NAD = 3,
n_noNAD = 2
)
Arguments
cmpds |
vector of compounds, including any standards |
time_points |
vector of time points |
n_NAD |
number of NAD positive samples. Default is 3 |
n_noNAD |
number of NAD negative samples. Default is 2 |
Details
Note that this function does not require plate object. It will create a plate object automatically and return MultiPlate object
Value
MultiPlate object
bioanalytic_app
Description
This function creates a shiny app for plate management
Usage
plate_app()
Value
A shiny app. No default return value. Can return a PlateObj if reuse_plate_button is clicked
Set plate description
Description
Set plate description
Usage
plate_metadata(plate, descr)
Arguments
plate |
PlateObj |
descr |
character. Description of the plate |
Value
PlateObj
Plotting 96 well plate
Description
Plotting 96 well plate
Usage
## S3 method for class 'PlateObj'
plot(
x,
color = "conc",
Instrument = "",
caption = "",
label_size = 1,
transform_dil = FALSE,
watermark = "auto",
path = NULL,
...
)
Arguments
x |
PlateObj |
color |
character. Coloring variable. Either "conc", "time", "factor", "samples", "dosage" |
Instrument |
A string placed at subtitle |
caption |
A string place at plate caption |
label_size |
numeric. Size of the label. Default is 15 |
transform_dil |
logical. If TRUE, transform the dilution factor to the label |
watermark |
character. If "auto", a watermark is added to the plot. If "none", no watermark is added. Default is "auto" |
path |
Default is NULL, if not null, must be a path to save plate image |
... |
additional arguments passed to ggplot2::ggsave |
Value
ggplot object
Examples
plate <- generate_96("new_plate", "C", 11) |>
add_blank(IS = FALSE, analyte = FALSE) |>
add_blank(IS = TRUE, analyte = FALSE) |>
add_samples(c(
"RD_per1", "RD_in1", "RD_T30", "RD_T60", "RD_T90", "RD_per2", "RD_in2",
"EE_in0", "EE_T30", "EE_in30", "EE_T60", "EE_in60", "EE_T90", "EE_in90"
))
plot(plate)
Plot the design of the plate
Description
Plot the design of the plate
Usage
plot_design(plate)
Arguments
plate |
PlateObj object |
Value
DiagrammeR object
Register a plate This will save the plate to the database
Description
Register a plate This will save the plate to the database
Usage
register_plate(plate)
Arguments
plate |
PlateObj object or MultiPlate object |
Value
PlateObj object or list of PlateObj objects
Register a multiple plates at once
Description
Register a multiple plates at once
Usage
## S4 method for signature 'MultiPlate'
register_plate(plate)
Arguments
plate |
MultiPlate object |
Value
a list of RegisteredPlate objects
Register a plate This will save the plate to the database
Description
Register a plate This will save the plate to the database
Usage
## S4 method for signature 'PlateObj'
register_plate(plate)
Arguments
plate |
PlateObj object |
Value
Registered PlateObj object
Write injection sequence to database
Description
Write injection sequence to database
Usage
write_injec_seq(injec_seq)
Arguments
injec_seq |
InjecListObj object |
Value
dataframe