Description Usage Arguments Value Examples
Function for calculating LOD
1 2 |
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 |
Returns a list containing LOD, LCL.LOD and UCL.LOD. If probit.plot == TRUE, also contains probit_fit, fitted_data and probit_plot.
1 2 3 | 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
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