find_LOQ: Function for calculating LOQ

Description Usage Arguments Value

View source: R/LOQ_bias_precision_functions.R

Description

Function for calculating LOQ

Usage

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find_LOQ(MRD, input_cancer_cells, threshold = 0.7, conf.level = 0.95,
  log = TRUE, log_offset = 1e-06, TE.plot = TRUE,
  sadler_params = list(b1 = 2, b2 = 0.1, b3 = -1.8), extra_sadler_log = F)

Arguments

MRD

The measured MRD values

input_cancer_cells

The pre-specified input. Note: can be frequency or any other input value

conf.level

Confidence level for calculating upper and lower bounds, default 0.95

log

Boolean for log10-transforming input_cancer_cells, default TRUE

log_offset

log offset for transformation to avoid log(0), default 1e-6

TE.plot

If TRUE, returns a ggplot of the Total Error fit

sadler_params

A list of initial values for sadler's fit

extra_sadler_log

Whether to take an extra log to improve Sadler fit stability; i.e.: log(y) ~ log(b1+b2*x)^b3)

prob

Detection probability for LOD, default 0.95

Value

Returns a list containing LOQ, LCL.LOQ and UCL.LOQ. Note that LCL.LOQ will almost always be NA; use LOD as the lower limit. If TE.plot == TRUE, also contains TE_fit, fitted_data and TE_plot.


AdaptiveCompBio/EOS documentation built on March 19, 2018, 3:13 a.m.