View source: R/import_atac_10x.R
DsATACsc.fragments | R Documentation |
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
)
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 |
maxFragsPerBarcode |
maximum number of fragments per barcode. Only barcodes with fewer fragments will be kept. [Only relevant if |
cellAnnot |
(optional) annotation table of all cells in the dataset. Must contain a |
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.). |
DsATACsc
object
Fabian Mueller
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