summarizeScores: Subtract scores of different samples.

In Repitools: Epigenomic tools

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

  ## 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

  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. 8, 2020, 7:52 p.m.