Title: | Easy Michaelis-Menten Enzyme Kinetics |
Version: | 0.2.4 |
Description: | Serves as a platform for published fluorometric enzyme assay protocols. 'ezmmek' calibrates, calculates, and plots enzyme activities as they relate to the transformation of synthetic substrates. At present, 'ezmmek' implements two common protocols found in the literature, and is modular to accommodate additional protocols. Here, these protocols are referred to as the In-Sample Calibration (Hoppe, 1983; <doi:10.3354/meps011299>) and In-Buffer Calibration (German et al., 2011; <doi:10.1016/j.soilbio.2011.03.017>). protocols. By containing multiple protocols, 'ezmmek' aims to stimulate discussion about how to best optimize fluorometric enzyme assays. A standardized approach would make studies more comparable and reproducible. |
License: | AGPL-3 |
Encoding: | UTF-8 |
Language: | en-US |
LazyData: | true |
RoxygenNote: | 7.1.1 |
Suggests: | knitr, rmarkdown, testthat |
VignetteBuilder: | knitr |
Imports: | magrittr, assertable, ggplot2, purrr, dplyr, nls2, rlang, tidyr |
NeedsCompilation: | no |
Packaged: | 2020-08-27 16:35:51 UTC; kanga |
Author: | Christopher Cook [aut, cre], Andrew Steen [aut] |
Maintainer: | Christopher Cook <ccook62@vols.utk.edu> |
Repository: | CRAN |
Date/Publication: | 2020-08-28 07:10:03 UTC |
ezmmek_calc_mm_fit
Description
Calculate Michaelis-Menten fit
Usage
ezmmek_calc_mm_fit(df, km, vmax)
Arguments
df |
Dataframe of class 'new_ezmmek_calibrate' |
km |
Starting value to estimate km. Default value is median of 'sub.conc' values |
vmax |
Starting value to estimate vmax. Default value is max activity calculated |
ezmmek_calc_std_lm_homo
Description
Calculate linear model for standard curve in homogenate
Usage
ezmmek_calc_std_lm_buffer(df)
Arguments
df |
Standard curve dataframe |
ezmmek_calc_std_lm_homo
Description
Calculate linear model for standard curve in homogenate
Usage
ezmmek_calc_std_lm_homo(df)
Arguments
df |
Standard curve dataframe |
ezmmek_calc_std_lm_homo_buffer
Description
Calculate linear model for standard curve in homogenate-buffer solution
Usage
ezmmek_calc_std_lm_homo_buffer(df)
Arguments
df |
Standard curve dataframe |
ezmmek_calibrate_activities
Description
Calibrates enzyme activity data by standard curve
Usage
ezmmek_calibrate_activities(df, method, columns)
Arguments
df |
Joined dataframes of class 'new_ezmmek_std_group' and 'new_ezmmek_act_group' |
method |
Enzyme assay protocol. Must define method as 'isc' or 'ibc' |
columns |
Column names carried from parent functions |
ezmmek_std_lm
Description
Creates dataframe of standard curve models as determined by grouping of user-defined columns
Usage
ezmmek_std_lm(df, method = method, columns = NULL)
Arguments
df |
Standard curve dataframe |
method |
Enzyme assay protocol. Defined in parent function |
columns |
Column names carried over from parent functions if parent functions used |
new_ezmmek_act_calibrate
Description
Creates dataframe containing calibrated enzyme activity data of class 'new_ezmmek_calibrate'
Usage
new_ezmmek_act_calibrate(
std.data.fn,
act.data.fn,
...,
method = NA,
columns = NULL
)
Arguments
std.data.fn |
Standard data file as character string |
act.data.fn |
Activity data file as character string |
... |
User defined column names to join std.data.fn and act.data.fn |
method |
Enzyme assay protocol. Must define method as 'isc' or 'ibc' |
columns |
Column names carried over from parent functions if parent functions used |
Examples
## Not run: new_obj <- new_ezmmek_act_calibrate("data/tyson_std_04172020.csv",
"data/tyson_sat_steen_04172020.csv",
site_name,
std_type,
method = "isc",
columns = NULL)
new_obj <- new_ezmmek_act_calibrate("data/tyson_std_04172020.csv",
"data/tyson_sat_german_04172020.csv",
site_name,
std_type,
method = "ibc",
columns = NULL)
## End(Not run)
new_ezmmek_act_group
Description
Groups raw activity data by user-defined columns
Usage
new_ezmmek_act_group(act.data.fn, ..., method = NA, columns = NULL)
Arguments
act.data.fn |
Activity data file as character string |
... |
User defined column names to join std.data.fn and act.data.fn |
method |
Enzyme assay protocol. Must define method as 'isc' or 'ibc' |
columns |
Column names carried over from parent functions if parent functions used |
Examples
## Not run: new_obj <- new_ezmmek_act_group("data/tyson_sat_steen_04172020.csv,
site_name,
std_type,
method = "isc",
columns = NULL)
new_obj <- new_ezmmek_act_group("data/tyson_sat_german_04172020.csv,
site_name,
std_type,
method = "ibc",
columns = NULL)
## End(Not run)
new_ezmmek_sat_fit
Description
Creates dataframe containing calibrated enzyme activity data and Michaelis-Menton fit of class 'new_ezmmek_sat_fit'
Usage
new_ezmmek_sat_fit(
std.data.fn,
act.data.fn,
...,
km = NULL,
vmax = NULL,
method = NA
)
Arguments
std.data.fn |
Standard data file as character string |
act.data.fn |
Activity data file as character string |
... |
User defined column names to join and group std.data.fn and act.data.fn |
km |
Starting value to estimate km. Default value is median of 'sub.conc' values |
vmax |
Starting value to estimate vmax. Default value is max activity calculated |
method |
Enzyme assay protocol. Must define method as 'isc' or 'ibc' |
Examples
## Not run: new_obj <- new_ezmmek_sat_fit("data/tyson_std_04172020.csv",
"data/tyson_sat_steen_04172020.csv",
site_name,
std_type,
km = NULL,
vmax = NULL,
method = "isc")
new_obj <- new_ezmmek_sat_fit("data/tyson_std_04172020.csv",
"data/tyson_sat_german_04172020.csv",
site_name,
std_type,
km = NULL,
vmax = NULL,
method = "ibc")
## End(Not run)
new_ezmmek_std_group
Description
Groups standard curve data by user-defined columns
Usage
new_ezmmek_std_group(std.data.fn, ..., method = NA, columns = NULL)
Arguments
std.data.fn |
Standard data file as character string |
... |
User defined column names to group std.data.fn |
method |
Enzyme assay protocol. Must define method as 'isc' or 'ibc' |
columns |
Column names carried over from parent functions if parent functions used |
Examples
## Not run: new_obj <- new_ezmmek_std_group("data/tyson_std_04172020.csv",
site_name,
std_type,
method = "isc",
columns = NULL)
new_obj <- new_ezmmek_std_group("data/tyson_std_04172020.csv",
site_name,
std_type,
method = "ibc",
columns = NULL)
## End(Not run)
plot_new_ezmmek_act_group
Description
Plots new_ezmmek_act_group object and facets by specified column names
Usage
## S3 method for class 'new_ezmmek_act_group'
plot(x, ...)
Arguments
x |
data.frame object of class new_ezmmek_act_group |
... |
User defined column names by which to facet plot |
Examples
## Not run: plot.new_ezmmek_act_group(new_ezmmek_act_group_obj,
site_name,
std_type)
## End(Not run)
plot_new_ezmmek_calibrate
Description
Plots new_ezmmek_calibrate object and facets by specified column names
Usage
## S3 method for class 'new_ezmmek_calibrate'
plot(x, ...)
Arguments
x |
data.frame object of class new_ezmmek_calibrate |
... |
User defined column names by which to facet plot |
Examples
## Not run: plot.new_ezmmek_calibrate(new_ezmmek_calibrate_obj,
site_name,
std_type)
## End(Not run)
plot_new_ezmmek_sat_fit
Description
Plots new_ezmmek_sat_fit object and facets by specified column names
Usage
## S3 method for class 'new_ezmmek_sat_fit'
plot(x, ...)
Arguments
x |
data.frame object of class new_ezmmek_sat_fit |
... |
User defined column names by which to facet plot |
Examples
## Not run: plot.new_ezmmek_act_group(new_ezmmek_sat_fit_obj,
site_name,
stdy_type)
## End(Not run)
plot_new_ezmmek_std_group
Description
Plots new_ezmmek_std_group object and facets by specified column names
Usage
## S3 method for class 'new_ezmmek_std_group'
plot(x, ...)
Arguments
x |
data.frame object of class new_ezmmek_std_group |
... |
User defined column names by which to facet plot |
Examples
## Not run: plot.new_ezmmek_std_group(new_ezmmek_std_group_obj,
site_name,
std_type)
## End(Not run)