extractRegion {MOCHA} | R Documentation |
extractRegion
Description
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. |
Value
countSE a SummarizedExperiment containing coverage for the given input cell populations.
Examples
## Not run:
countSE <- MOCHA::extractRegion(
SampleTileObj = SampleTileMatrices,
cellPopulations = "ALL",
region = "chr1:18137866-38139912",
numCores = 30,
sampleSpecific = FALSE
)
## End(Not run)