grofit: grofit: Extract physiological parameters from kinetic OD600...

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

Description

grofit takes OD600 data from a specific format 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 column percent_NA_od600 contains the percent of time points that were NA for a given well.

Usage

grofit(gropro_output)

Arguments

gropro_output

This is a tidy dataframe containing columns exactly named Sample.ID, Time, and OD600 at a 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.

Model fit:

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

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

Examples

### grofit ###
## Not run: grofit_output = grofit(gropro_output)

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