Export insertion counts to per-sample BigWig files after applying a rolling sum and rolling median smoothing filter.
Source:R/exportSmoothedInsertions.R
exportSmoothedInsertions.Rd
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.