DsATACsc.fragments

Create a DsATACsc dataset from multiple input fragment files

DsATACsc.fragments(
  sampleAnnot,
  fragmentFiles,
  genome,
  regionSets = NULL,
  sampleIdCol = NULL,
  minFragsPerBarcode = 500L,
  maxFragsPerBarcode = Inf,
  cellAnnot = NULL,
  keepInsertionInfo = FALSE,
  diskDump.fragments = keepInsertionInfo,
  cellQcStats = TRUE
)

Arguments

sampleAnnot

data.frame specifying the sample annotation table

fragmentFiles

vector of fragment files or the column name in the sample annotation table containing thse file names. fragment files must be tab-separated with columns "chrom", "chromStart", "chromEnd", "barcode" and "duplicateCount" and must not contain a header line

genome

genome assembly

regionSets

a list of GRanges objects which contain region sets over which count data will be aggregated

sampleIdCol

column name or index in the sample annotation table containing unique sample identifiers

minFragsPerBarcode

minimum number of fragments required for a barcode to be kept. [Only relevant if cellAnnot==NULL]

maxFragsPerBarcode

maximum number of fragments per barcode. Only barcodes with fewer fragments will be kept. [Only relevant if cellAnnot==NULL]

cellAnnot

(optional) annotation table of all cells in the dataset. Must contain a 'cellId' and 'cellBarcode' columns.

keepInsertionInfo

flag indicating whether to maintain the insertion information in the resulting object.

diskDump.fragments

Keep fragment coordinates stored on disk rather than in main memory. This saves memory, but increases runtime and I/O.

cellQcStats

flag indicating whether to compute additional cell QC statistics (TSS enrichment, etc.).

Value

DsATACsc object

Author

Fabian Mueller