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Calculate a GR value.

Source: R/calculate_GR_value.R
calculate_GR_value.Rd

Calculate a GR value for a given set of dose response values.

Usage

calculate_GR_value(
  rel_viability,
  corrected_readout,
  day0_readout,
  untrt_readout,
  ndigit_rounding,
  duration,
  ref_div_time,
  cap = 1.25
)

calculate_time_dep_GR_value(
  corrected_readout,
  day0_readout,
  untrt_readout,
  ndigit_rounding
)

calculate_endpt_GR_value(
  rel_viability,
  duration,
  ref_div_time,
  cap = 1.25,
  ndigit_rounding
)

Arguments

rel_viability

numeric vector representing the Relative Viability.

corrected_readout

numeric vector containing the corrected readout.

day0_readout

numeric vector containing the day 0 readout.

untrt_readout

numeric vector containing the untreated readout.

ndigit_rounding

integer specifying the number of digits to use for calculation rounding.

duration

numeric value specifying the length of time the cells were treated (in hours).

ref_div_time

numeric value specifying the reference division time for the cell line in the experiment.

cap

numeric value representing the value to cap the highest allowed relative viability at.

Value

numeric vector containing GR values, one value for each element of the input vectors.

Details

Note that this function expects that all numeric vectors are of the same length. calculate_GR_value will try to greedily calculate a GR value. If no day 0 readouts are available, the duration and ref_div_time will be used to try to back-calculate a day 0 value in order to produce a GR value.

In the case of calculating the reference GR value from multiple reference readout values, the vectorized calculation is performed and then the resulting vector should be averaged outside of this function.

Note that it is expected that the ref_div_time and duration are reported in the same units.

See also

normalize_SE2

Examples


duration <- 144
rv <- seq(0.1, 1, 0.1)
corrected <- seq(41000, 50000, 1000)
day0 <- seq(91000, 95500, 500)
untrt <- rep(c(115000, 118000), 5)

calculate_GR_value(
  rel_viability = rv,
  corrected_readout = corrected,
  day0_readout = day0,
  untrt_readout = untrt,
  ndigit_rounding = 4,
  duration = duration,
  ref_div_time = duration / 2
)
#>  [1] -0.9057 -0.8802 -0.9058 -0.8794 -0.9065 -0.8791 -0.9077 -0.8793 -0.9095
#> [10] -0.8800

readouts <- rep(10000, 5)
calculate_time_dep_GR_value(readouts, readouts * 1.32, readouts * 2, 2)
#> [1] -0.37 -0.37 -0.37 -0.37 -0.37

readouts <- rep(10000, 5)
calculate_endpt_GR_value(readouts, 72, 1, ndigit_rounding = 2)
#> [1] 1.01 1.01 1.01 1.01 1.01