Export normalized coverage files to per-sample or sample-averaged (per cell population) BigWig files.
Source:R/exportCoverage.R
exportCoverage.Rd
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.