summarizeScores: Subtract scores of different samples.

Description Usage Arguments Value Author(s) Examples

Description

Based on a design matrix, scores matrices are subtracted, and a new ScoresList is returned, with the scores of the contrasts in it.

Usage

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  ## S4 method for signature 'ScoresList,matrix'
summarizeScores(scores.list, design, verbose = TRUE)

Arguments

scores.list

A ScoresList object describing the coverage or intensity scores of a set of samples.

design

A matrix that contains only -1, 0, or 1.

verbose

Whether to print a statement explaining the function was called.

Value

A ScoresList object holding the scores of the contrasts that were specified by the design matrix.

Author(s)

Dario Strbenac

Examples

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  data(chr21genes)
  data(samplesList)  # Loads 'samples.list.subset'.

  fs <- featureScores(samples.list.subset[1:2], chr21genes, up = 2000, down = 1000,
                      freq = 500, s.width = 500)
  d.matrix <- matrix(c(-1, 1))
  colnames(d.matrix) <- "IP-input"
  summarizeScores(fs, d.matrix)

Repitools documentation built on Nov. 17, 2017, 12:46 p.m.