exportCoverage {MOCHA}

exportCoverage

Description

exportCoverage will export normalized coverage files to BigWig files, either as sample-specific or sample-averaged files, for visualization in genome browsers.

Usage

exportCoverage(
  SampleTileObject,
  dir = getwd(),
  type = TRUE,
  cellPopulations = "ALL",
  groupColumn = NULL,
  subGroups = NULL,
  sampleSpecific = FALSE,
  saveFile = TRUE,
  numCores = 1,
  verbose = FALSE
)

Arguments

SampleTileObject

The SummarizedExperiment object output from getSampleTileMatrix

dir

string. Directory to save files to.

type

Boolean. Default is TRUE, and exports Coverage. If set to FALSE, exports Insertions.

cellPopulations

vector of strings. Cell subsets for which to call peaks. This list of group names must be identical to names that appear in the SampleTileObject. Optional, if cellPopulations='ALL', then peak calling is done on all cell populations. Default is 'ALL'.

groupColumn

Optional, the column containing sample group labels for returning coverage within sample groups. Default is NULL, all samples will be used.

subGroups

a list of subgroup(s) within the groupColumn from the metadata. Optional, default is NULL, all labels within groupColumn will be used.

sampleSpecific

If TRUE, a BigWig will export for each sample-cell type combination.

saveFile

Boolean. If TRUE, it will save to a BigWig. If FALSE, it will return the GRangesList without writing a BigWig.

numCores

integer. Number of cores to parallelize peak-calling across multiple cell populations

verbose

Set TRUE to display additional messages. Default is FALSE.

Value

countSE a SummarizedExperiment containing coverage for the given input cell populations.

Examples

## Not run: 
MOCHA::exportCoverage(
  SampleTileObject = SampleTileMatrices,
  cellPopulations = "ALL",
  numCores = 30,
  sampleSpecific = FALSE
)

## End(Not run)