exportSmoothedInsertions {MOCHA}

exportSmoothedInsertions

Description

exportSmoothedInsertions Takes a SampleTileMatrix with linked insertion files and applies a smoothing filter (a rolling sum then rolling median) to the insertions, finally exporting the smoothed insertion files to bigwig format.

Usage

exportSmoothedInsertions(
  SampleTileObj,
  cellPopulation,
  outDir = NULL,
  sumWidth = 10,
  medianWidth = 11,
  force = FALSE,
  slow = FALSE,
  verbose = FALSE
)

Arguments

SampleTileObj

A MultiAssayExperiment or RangedSummarizedExperiment from MOCHA

cellPopulation

A string denoting the cell population of interest

outDir

Directory to write output bigwig files. Default is NULL, where the directory in 'SampleTileObj@metadata$Directory' will be used.

sumWidth

Window size for rolling sum in basepairs. Default is 10.

medianWidth

Window size for rolling median in basepairs. Must be odd. Default is 11.

force

Set TRUE to overwrite existing files. Default is FALSE.

slow

Set TRUE to bypass optimisations and compute smoothing filter directly on the whole genome. May run slower and consume more RAM. Default is FALSE.

verbose

Set TRUE to display additional messages. Default is FALSE.

Value

outPaths List of paths of exported insertion files

Examples

## Not run: 
# Depends on and manipulates files on filesystem
outPath <- MOCHA::exportSmoothedInsertions(
  SampleTileObj,
  cellPopulation = "CD4 Naive", sumWidth = 10, medianWidth = 11, verbose = FALSE
)

## End(Not run)