find_LOD: Function for calculating LOD

In AdaptiveCompBio/EOS: Commonly used functions for the EOS project

Description

Function for calculating LOD

Usage

find_LOD(MRD, input_cancer_cells, prob = 0.95, conf.level = 0.95,
  log = TRUE, log_offset = 1e-06, probit.plot = TRUE)

Arguments

MRD	The measured MRD values
input_cancer_cells	The pre-specified input. Note: can be frequency or any other input value
prob	Detection probability for LOD, default 0.95
conf.level	Confidence level for calculating upper and lower bounds, default 0.95
log	Boolean for log10-transforming MRD and input_cancer_cells, default TRUE
log_offset	If log transforming, offset value for the MRD to avoid log(0) issues, default 0
probit.plot	If TRUE, returns a ggplot of the probit fit

Value

Returns a list containing LOD, LCL.LOD and UCL.LOD. If probit.plot == TRUE, also contains probit_fit, fitted_data and probit_plot.

Examples

Datain <- read.table("processed_data/20171119_MVP-00147_lod_data-table1.tsv", head=TRUE, as.is=TRUE, sep="\t")
find_LOD(Datain$Sample.MRD.Frequency, Datain$Input.Cancer.Cells, probit.plot=F)$LOD
[1] 2.289792

AdaptiveCompBio/EOS documentation built on May 26, 2019, 6:37 a.m.