ap_cutoff_selection2: Cutoff selection

In cekehe/rappp: QC, data transformation and visualization for PAPP

Cutoff selection

Description

Select cutoff based on the slope of the density of scores per antigen.

Usage

ap_cutoff_selection2(
  x,
  slope_cutoff = -0.5,
  offset = 0.1,
  bw = 0.1,
  check.names = FALSE
)

Arguments

x	List with at least two elements, see Details for naming and content. It is recommended to use the output from ap_scoring2().
slope_cutoff	Arbitrary slope cutoff value. Can be chosen freely.
offset	Offset used to prevent script from finding the peak (as slope = 0 there).
bw	Bandwidth for density funciton, default set to 0.1.
check.names	logical, altered default from data.frame().

Details

A cutoff will be selected for each antigen based on the distribution of the scores for the antigen. The algorithm will search for a local min nearest the highest peak in a density plot using bandwidth=0.1. The input data will also be transformed into binary data based on the iterated cutoffs.

Only samples that passed previous QC-filtering will be included when iterating the cutoff, but if more samples are included in the input data all will be transformed to binary data so that reactivities in for example control wells can be assessed as well.

The x list needs to include at least the element:

SCORE = scored data,

CUTOFF_KEY = Cutoff key as data.frame with cutoff values, scores and colors.

SAMPLES = Sample info, if any should be excluded then these should be annotated in a column called "Filtered". Any samples with no text (ie. "" or NA) in such column will be included.

Value

Updated input x with the new list elements

DENS = Density output used for cutoff selection,

ANTIGEN_CUTOFFS_CONT = Calculated antigen specific cutoffs, continues values,

ANTIGEN_CUTOFFS = Calculated antigen specific cutoffs, translated into the descrete cutoff steps,

BINARY_CO = Binary table based on the antigen specific cutoffs.

cekehe/rappp documentation built on May 17, 2022, 8:54 a.m.