MOCHA (version 1.1.0)

extractRegion: 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
)

Value

countSE a SummarizedExperiment containing coverage for the given input cell populations.

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.

Examples

if (FALSE) {
countSE <- MOCHA::extractRegion(
  SampleTileObj = SampleTileMatrices,
  cellPopulations = "ALL",
  region = "chr1:18137866-38139912",
  numCores = 30,
  sampleSpecific = FALSE
)
}