exportCoverage {MOCHA} | R Documentation |
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)