extractRegion
will extract the coverage files created by
callOpenTiles and return a specific region's coverage
Usage
extractRegion(
SampleTileObj,
type = TRUE,
region,
cellPopulations = "ALL",
groupColumn = NULL,
subGroups = NULL,
sampleSpecific = FALSE,
approxLimit = 1e+05,
binSize = 250,
sliding = NULL,
numCores = 1,
verbose = FALSE
)
Arguments
- SampleTileObj
The SummarizedExperiment object output from getSampleTileMatrix
- type
Boolean. Default is true, and exports Coverage. If set to FALSE, exports Insertions.
- region
a GRanges object or vector or strings containing the regions of interest. Strings must be in the format "chr:start-end", e.g. "chr4:1300-2222".
- 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 SampleTileObj. 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, get a sample-specific count dataframe out. Default is FALSE, average across samples and get a dataframe out.
- approxLimit
Optional limit to region size, where if region is larger than approxLimit basepairs, binning will be used. Default is 100000.
- binSize
Optional numeric, size of bins in basepairs when binning is used. Default is 250.
- sliding
Optional numeric. Default is NULL. This number is the size of the sliding window for generating average intensities.
- numCores
integer. Number of cores to parallelize peak-calling across multiple cell populations
- verbose
Set TRUE to display additional messages. Default is FALSE.