calf: calf

Description Usage Arguments Value Examples

View source: R/calf_wrappers.R

Description

Coarse approximation linear function

Usage

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calf(data, nMarkers, targetVector, margin, optimize = "pval",
  verbose = FALSE)

Arguments

data

Matrix or data frame. First column must contain case/control dummy coded variable (if targetVector = "binary"). Otherwise, first column must contain real number vector corresponding to selection variable (if targetVector = "real"). All other columns contain relevant markers.

nMarkers

Maximum number of markers to include in creation of sum.

targetVector

Indicate "binary" for target vector with two options (e.g., case/control). Indicate "real" for target vector with real numbers.

margin

Real number from 0 to 1. Indicates the amount a potential marker must improve the target criterion (Pearson correlation or p-value) in order to add the marker.

optimize

Criteria to optimize if targetVector = "binary." Indicate "pval" to optimize the p-value corresponding to the t-test distinguishing case and control. Indicate "auc" to optimize the AUC.

verbose

Logical. Indicate TRUE to print activity at each iteration to console. Defaults to FALSE.

Value

A data frame containing the chosen markers and their assigned weight (-1 or 1)

The AUC value for the classification

rocPlot. A plot object from ggplot2 for the receiver operating curve.

Examples

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calf(data = CaseControl, nMarkers = 6, targetVector = "binary")

CALF documentation built on May 29, 2017, 7:54 p.m.