calculate_growthrate_from_defined_time

calculates growth rate and generation time from user-defined log-phase start and end time.

calculate_growthrate_from_defined_time(
  dat_growth_curve,
  logphase_tibble,
  average_replicates = FALSE,
  select_replicates = NULL
)

Arguments

dat_growth_curve	a tibble, with first column as `Time` and after that columns as samples. Samples should be named as `sampleName_replicate`, for example `CgFlu_R1` , `CgFlu_R2`, `CgFlu_R3`. If data does not contain replicates then sample name should be `CgFlu_R1`, `Cg_R1`, `YPD_R1` The function assumes that data contains OD values in increasing order.
logphase_tibble	a tibble, containing pre-defined logphase start and end time point. It must contain three columns with first column of condition or sample and second and third column of start and end. The condition column must match with sample names of `dat_growth_curve`
average_replicates	logical, to calculate growth rates as average of replicates, Default: FALSE
select_replicates	a vector, define replicates to be selected to plot, it should be anything after `_`. for eg. if only replicate R1 and R2 need to be plotted from samples CgFlu_R1, CgFlu_R2; the vector should be `c("R1", "R2")`, Default: NULL
cells_at_OD_1	numeric, a mutplication factor to use absolute cell number at OD=1, for instance OD600=1 represents 3e+07 yeast cells. Default: 3e+07

Value

a tibble, containing growth rate (generation/hour) and generation time or doubling time (minutes/generation)

Details

User defined start and end logphase time-points are used to compute growth_rate. For average of replicates, mean of OD and time-points is computed.

Examples

if (FALSE) {
if(interactive()){

 # Load logphase start-end from local file
 logphase_dat <- system.file("extdata", "logphase_for_replicates.txt", package = "growkar")
 logphase_tibble <- readr::read_delim(logphase_dat, delim="\t", col_names = TRUE)

 # Compute growth_rate
 calculate_growthrate_from_defined_time(dat_growth_curve = growkar::yeast_growth_data,logphase_tibble = logphase_tibble, average_replicates = TRUE)

 }
}