| Title: | Easy Michaelis-Menten Enzyme Kinetics |
|---|---|
| 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. |
| Authors: | Christopher Cook [aut, cre], Andrew Steen [aut] |
| Maintainer: | Christopher Cook <[email protected]> |
| License: | AGPL-3 |
| Version: | 0.2.4 |
| Built: | 2025-03-13 04:16:53 UTC |
| Source: | https://github.com/cran/ezmmek |
Calculate Michaelis-Menten fit
ezmmek_calc_mm_fit(df, km, vmax)ezmmek_calc_mm_fit(df, km, vmax)
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 |
Calculate linear model for standard curve in homogenate
ezmmek_calc_std_lm_buffer(df)ezmmek_calc_std_lm_buffer(df)
df |
Standard curve dataframe |
Calculate linear model for standard curve in homogenate
ezmmek_calc_std_lm_homo(df)ezmmek_calc_std_lm_homo(df)
df |
Standard curve dataframe |
Calculate linear model for standard curve in homogenate-buffer solution
ezmmek_calc_std_lm_homo_buffer(df)ezmmek_calc_std_lm_homo_buffer(df)
df |
Standard curve dataframe |
Calibrates enzyme activity data by standard curve
ezmmek_calibrate_activities(df, method, columns)ezmmek_calibrate_activities(df, method, columns)
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 |
Creates dataframe of standard curve models as determined by grouping of user-defined columns
ezmmek_std_lm(df, method = method, columns = NULL)ezmmek_std_lm(df, method = method, columns = NULL)
df |
Standard curve dataframe |
method |
Enzyme assay protocol. Defined in parent function |
columns |
Column names carried over from parent functions if parent functions used |
Creates dataframe containing calibrated enzyme activity data of class 'new_ezmmek_calibrate'
new_ezmmek_act_calibrate( std.data.fn, act.data.fn, ..., method = NA, columns = NULL )new_ezmmek_act_calibrate( std.data.fn, act.data.fn, ..., method = NA, columns = NULL )
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 |
## 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)## 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)
Groups raw activity data by user-defined columns
new_ezmmek_act_group(act.data.fn, ..., method = NA, columns = NULL)new_ezmmek_act_group(act.data.fn, ..., method = NA, columns = NULL)
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 |
## 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)## 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)
Creates dataframe containing calibrated enzyme activity data and Michaelis-Menton fit of class 'new_ezmmek_sat_fit'
new_ezmmek_sat_fit( std.data.fn, act.data.fn, ..., km = NULL, vmax = NULL, method = NA )new_ezmmek_sat_fit( std.data.fn, act.data.fn, ..., km = NULL, vmax = NULL, method = NA )
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' |
## 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)## 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)
Groups standard curve data by user-defined columns
new_ezmmek_std_group(std.data.fn, ..., method = NA, columns = NULL)new_ezmmek_std_group(std.data.fn, ..., method = NA, columns = NULL)
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 |
## 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)## 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)
Plots new_ezmmek_act_group object and facets by specified column names
## S3 method for class 'new_ezmmek_act_group' plot(x, ...)## S3 method for class 'new_ezmmek_act_group' plot(x, ...)
x |
data.frame object of class new_ezmmek_act_group |
... |
User defined column names by which to facet plot |
## Not run: plot.new_ezmmek_act_group(new_ezmmek_act_group_obj, site_name, std_type) ## End(Not run)## Not run: plot.new_ezmmek_act_group(new_ezmmek_act_group_obj, site_name, std_type) ## End(Not run)
Plots new_ezmmek_calibrate object and facets by specified column names
## S3 method for class 'new_ezmmek_calibrate' plot(x, ...)## S3 method for class 'new_ezmmek_calibrate' plot(x, ...)
x |
data.frame object of class new_ezmmek_calibrate |
... |
User defined column names by which to facet plot |
## Not run: plot.new_ezmmek_calibrate(new_ezmmek_calibrate_obj, site_name, std_type) ## End(Not run)## Not run: plot.new_ezmmek_calibrate(new_ezmmek_calibrate_obj, site_name, std_type) ## End(Not run)
Plots new_ezmmek_sat_fit object and facets by specified column names
## S3 method for class 'new_ezmmek_sat_fit' plot(x, ...)## S3 method for class 'new_ezmmek_sat_fit' plot(x, ...)
x |
data.frame object of class new_ezmmek_sat_fit |
... |
User defined column names by which to facet plot |
## Not run: plot.new_ezmmek_act_group(new_ezmmek_sat_fit_obj, site_name, stdy_type) ## End(Not run)## Not run: plot.new_ezmmek_act_group(new_ezmmek_sat_fit_obj, site_name, stdy_type) ## End(Not run)
Plots new_ezmmek_std_group object and facets by specified column names
## S3 method for class 'new_ezmmek_std_group' plot(x, ...)## S3 method for class 'new_ezmmek_std_group' plot(x, ...)
x |
data.frame object of class new_ezmmek_std_group |
... |
User defined column names by which to facet plot |
## Not run: plot.new_ezmmek_std_group(new_ezmmek_std_group_obj, site_name, std_type) ## End(Not run)## Not run: plot.new_ezmmek_std_group(new_ezmmek_std_group_obj, site_name, std_type) ## End(Not run)