simpleCutPoint: Simple Cutpoint estimation

In genomaths/MethylIT: Methylation Analysis Based on Signal Detection

Simple Cutpoint estimation

Description

Internal function to estimate simple cutpoint according to Youden Index.

Usage

simpleCutPoint(
  LR,
  control.names,
  treatment.names,
  column,
  div.col,
  tv.col = NULL,
  tv.cut,
  clas.perf,
  classifier,
  interactions = NULL,
  n.pc,
  prop,
  post.cut = 0.5,
  maxnodes = NULL,
  ntree = 400,
  nsplit = 1L,
  cutp_data = FALSE,
  num.cores,
  tasks,
  ...
)

Arguments

LR, res, control.names, treatment.names, column, div.col	Same as in estimateCutPoint
column, div.col, tv.col, tv.cut, clas.perf	Same as in estimateCutPoint
classifier, n.pc, prop, cutp_data, num.cores, tasks	Same as in estimateCutPoint
interactions	If a logistic classifier is used. Variable interactions to consider in a logistic regression model. Any pairwise combination of the variable 'hdiv', 'TV', 'wprob', and 'pos' can be provided. For example: 'hdiv:TV', 'wprob:pos', 'wprob:TV', etc.

Details

This function is called by function estimateCutPoint.

Value

Specified in function estimateCutPoint for parameter setting simple = TRUE

Examples

## Get a set of potential DMPS (PS)
data(PS, package = 'MethylIT')

cutp <- simpleCutPoint(LR = PS, column = c(hdiv = TRUE, TV = TRUE,
                                           wprob = TRUE, pos = TRUE),
                       classifier = 'qda', n.pc = 4,
                       control.names = c('C1', 'C2', 'C3'),
                       treatment.names = c('T1', 'T2', 'T3'),
                       tv.cut = 0.5, clas.perf = TRUE, prop = 0.6,
                       div.col = 9L)

cutp

genomaths/MethylIT documentation built on Feb. 3, 2024, 1:24 a.m.