getSequencingBias {MOCHA}

getSequencingBias

Description

getSequencingBias takes the output of peak calling with callOpenTiles and creates sample-tile matrices containing the signal intensity at each tile.

Usage

getSequencingBias(
  SampleTileObj,
  cellPopulations = "all",
  cellPopulation,
  groupColumn,
  foreground,
  background,
  verbose = TRUE
)

Arguments

SampleTileObj

a SummarizedExperiment object generated by MOCHA

cellPopulations

vector of strings. Cell subsets found in the TSAM, or the word 'All' if all should be used.

cellPopulation

A string denoting the cell population of interest

groupColumn

The column containing sample group labels

foreground

The foreground group of samples for differential comparison

background

The background group of samples for differential comparison

verbose

Set TRUE to display additional messages. Default is FALSE.

Value

plot object