biclust (version 2.0.3.1)

binarize: Binarize

Description

Methods to convert a real matrix to a binary matrix.

Usage

binarize(x, threshold=NA)
binarizeByPercentage(x,percentage, error=0.2, gap=0.1)
densityOnes(x)

Arguments

x

The data matrix to be binarized.

threshold

Threshold used to binarize. Values over threshold will be set to 1, the rest to 0. If threshold is NA, median is used as threshold. Default NA.

percentage

Percentage of ones against zeros desired in the binary matrix.

error

Percentage of ones against zeros in the final matrix will be in [percentage-error, percentage+error]. Default 0.2

gap

Value used for incremental search of threshold. Default 0.1

Author

Rodrigo Santamaria

Details

The binarize function returns a matrix binarized by input threshold, or by the median if no threshold is given.

The binarizeByPercentage function returns a matrix binarize by input percentage, given as desired density of ones against zeros.

The densityOnes function returns the percentage of ones against zeros in a logical matrix

Examples

  data(BicatYeast)
  m1=binarize(BicatYeast)
  m2=binarize(BicatYeast, 0.2)
  m3=binarizeByPercentage(BicatYeast, 5)
  densityOnes(m3)
  densityOnes(m2)
  densityOnes(m1)
  drawHeatmap(BicatYeast)
  drawHeatmap(m1)
  drawHeatmap(m2)
  drawHeatmap(m3)