callOpenTiles {MOCHA}

callOpenTiles Perform peak-calling on a set of fragments or an ArchR Project.

Description

callOpenTiles is the main peak-calling function in MOCHA that serves as a wrapper function to call peaks provided a set of fragment files and an ArchR Project for meta-data purposes

Usage

callOpenTiles(
  ATACFragments,
  cellColData,
  blackList,
  genome,
  cellPopLabel,
  cellPopulations = "ALL",
  studySignal = NULL,
  generalizeStudySignal = FALSE,
  cellCol = "RG",
  TxDb,
  OrgDb,
  outDir,
  numCores = 30,
  verbose = FALSE,
  force = FALSE
)

## S4 method for signature 'GRangesList'
callOpenTiles(
  ATACFragments,
  cellColData,
  blackList,
  genome,
  cellPopLabel,
  cellPopulations = "ALL",
  studySignal = NULL,
  generalizeStudySignal = FALSE,
  cellCol = "RG",
  TxDb,
  OrgDb,
  outDir,
  numCores = 30,
  verbose = FALSE,
  force = FALSE
)

## S4 method for signature 'list'
callOpenTiles(
  ATACFragments,
  cellColData,
  blackList,
  genome,
  cellPopLabel,
  cellPopulations = "ALL",
  studySignal = NULL,
  generalizeStudySignal = FALSE,
  cellCol = "RG",
  TxDb,
  OrgDb,
  outDir,
  numCores = 30,
  verbose = FALSE,
  force = FALSE
)

.callOpenTiles_ArchR(
  ATACFragments,
  cellPopLabel,
  cellPopulations = "ALL",
  studySignal = NULL,
  generalizeStudySignal = FALSE,
  TxDb,
  OrgDb,
  outDir = NULL,
  numCores = 30,
  verbose = FALSE,
  force = FALSE
)

Arguments

ATACFragments

an ArchR Project, or a GRangesList of fragments. Each GRanges in the GRanges list must have unique cell IDs in the column given by 'cellCol'.

cellColData

A DataFrame containing cell-level metadata. This must contain both a column 'Sample' with unique sample IDs and the column specified by 'cellPopLabel'.

blackList

A GRanges of blacklisted regions

genome

A BSgenome object, or the full name of an installed BSgenome data package, or a short string specifying the name of an NCBI assembly (e.g. "GRCh38", "TAIR10.1", etc...) or UCSC genome (e.g. "hg38", "bosTau9", "galGal6", "ce11", etc...). The supplied short string must refer unambiguously to an installed BSgenome data package. See getBSgenome.

cellPopLabel

string indicating which column in the ArchRProject metadata contains the cell population label.

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 ArchRProject metadata. Optional, if cellPopulations='ALL', then peak calling is done on all cell populations in the ArchR project metadata. Default is 'ALL'.

studySignal

The median signal (number of fragments) in your study. If not set, this will be calculated using the input ArchR project but relies on the assumption that the ArchR project encompasses your whole study (i.e. is not a subset).

generalizeStudySignal

If 'studySignal' is not provided, calculate the signal as the mean of the mean & median number of fragments for of individual samples within each cell population. This may improve MOCHA's ability to generalize to datasets with XXXXXX #TODO. Default is FALSE, use the median number of fragments.

cellCol

The column in cellColData specifying unique cell ids or barcodes. Default is "RG", the unique cell identifier used by ArchR.

TxDb

The exact package name of a TxDb-class transcript annotation package for your organism (e.g. "TxDb.Hsapiens.UCSC.hg38.refGene"). This must be installed. See Bioconductor AnnotationData Packages.

OrgDb

The exact package name of a OrgDb-class genome wide annotation package for your organism (e.g. "org.Hs.eg.db"). This must be installed. See Bioconductor AnnotationData Packages

outDir

is a string describing the output directory for coverage files. Must be a complete directory string. With ArchR input, set outDir to NULL to create a directory within the input ArchR project directory named MOCHA for saving files.

numCores

integer. Number of cores to parallelize peak-calling across multiple cell populations.

verbose

Set TRUE to display additional messages. Default is FALSE.

force

Optional, whether to force creation of coverage files if they already exist. Default is FALSE.

Value

tileResults A MultiAssayExperiment object containing ranged data for each tile

Examples

## Not run: 
# Starting from an ArchR Project:
tileResults <- MOCHA::callOpenTiles(
  ArchRProj = myArchRProj,
  cellPopLabel = "celltype_labeling",
  cellPopulations = "CD4",
  TxDb = "TxDb.Hsapiens.UCSC.hg38.refGene",
  OrgDb = "org.Hs.eg.db",
  numCores = 1
)

## End(Not run)

# Starting from GRangesList
if (
  requireNamespace("BSgenome.Hsapiens.UCSC.hg19") &&
    requireNamespace("TxDb.Hsapiens.UCSC.hg38.refGene") &&
    requireNamespace("org.Hs.eg.db")
) {
  tiles <- MOCHA::callOpenTiles(
    ATACFragments = MOCHA::exampleFragments,
    cellColData = MOCHA::exampleCellColData,
    blackList = MOCHA::exampleBlackList,
    genome = "BSgenome.Hsapiens.UCSC.hg19",
    TxDb = "TxDb.Hsapiens.UCSC.hg38.refGene",
    OrgDb = "org.Hs.eg.db",
    outDir = tempdir(),
    cellPopLabel = "Clusters",
    cellPopulations = c("C2", "C5"),
    numCores = 1
  )
}