phgrofit: phgrofit: Extract physiological parameters from kinetic pH...

In Kaleido-Biosciences/phgrofit: Extracting Physiological Data From Kinetic OD600 and pH Curves

Description

phgrofit takes pH and OD600 data that has been formated by phgropro and applies a smoothing spline to extract relevant physiological data. Importantly, this function drops any NA values that may exist when fitting the spline. These values occasionally occur when measuring pH, either from an erratic read or if the pH is outside of the standard curve. The columns percent_NA_od600 and percent_NA_pH contain the percent of timepoints that were NA for a given well.

Usage

phgrofit(phgropro_output)

Arguments

phgropro_output

This is the output of phgropro which is a tidy dataframe containing columns exactly named Sample.ID, Time, OD600, and pH at minimum. There may also be any other columns representing any other metadata.

Value

A tidy data frame of several features that were extracted from a smoothing spline fit. The data frame also contains information that can be used to assess model fit. Physiologial features:

• "starting_od600"This is the starting od600

• "od600_lag_length"This is the length of the calculated lag phase. Calculated by determining the time where the tangent line at the point of the max growth rate meets the starting od600

• "od600_max_gr" This is the maximum growth rate that is observed. Calculated by determining the max derivitive of the spline fit for OD600

• "max_od600" This is the maximum od600 observed by the spline fit

• "difference_between_max_and_end_od600" This is the difference between the maximum and end od600. Higher values should correspond to a "death phase". Or one could argue the cells are getting smaller.

• "auc_od600"This is the area under the curve of the OD600 curves. It is calculated using the trapezoidal rule on fitted values from smooth.spline.

• "starting_pH"This is the starting pH

• "max acidification rate" This is the max acidification rate observed in the spline fit. Calculated by determining the min derivitive of the spline fit for pH.

• "min pH" This is the minimum pH that is observed in the spline fit.

• "time_of_min_pH " This is the time that the minimum pH occurs in the spline fit.

• "max_basification_rate" This is the max basification rate observed in the spline fit. Calculated by determining the max derivitive of the spline fit for pH.

• "max_pH" This is the max pH observed in the spline fit.

• "difference_between_end_and_min_pH" This is the difference between the end and the minimum pH. A higher value corresponds to a greater pH increase. Higher values may reflect an increased proteolytic state

• "auc_pH"This is the area under the curve of the pH curves. It is calculated using the trapezoidal rule on fitted values from smooth.spline.

Model fit:

• "percent_NA_od600"The percent of wells that were NA when fitting the spline to the kinetic od600 data

• "percent_NA_pH"The percent of wells that were NA when fitting the spline to the kinetic pH data

• "rmse_od600"The Root-mean-square deviation for od600

• "rmse_pH"The Root-mean-square deviation for pH

Examples

### phgropro processing
## Not run:  phgropro_output = phgropro(biotek_export = filepath.txt,metadata = metadata.csv,Plate_Type = 96)

### phgrofit processing
## Not run: phgrofit_output = phgrofit(phgropro_output)

Kaleido-Biosciences/phgrofit documentation built on Feb. 8, 2022, 5:16 a.m.