View source: R/import_atac_10x.R
DsATAC.cellranger | R Documentation |
Create a DsATAC dataset from multiple input files output by 10x cellranger
DsATAC.cellranger(
sampleAnnot,
sampleDirPrefixCol,
genome,
dataDir = "",
regionSets = NULL,
addPeakRegions = TRUE,
sampleIdCol = sampleDirPrefixCol,
keepInsertionInfo = FALSE,
diskDump.fragments = keepInsertionInfo
)
sampleAnnot |
data.frame specifying the sample annotation table |
sampleDirPrefixCol |
column name specifying the directory prefix for each sample in the sample annotation table |
genome |
genome assembly |
dataDir |
directory where the files are located |
regionSets |
a list of GRanges objects which contain region sets over which count data will be aggregated |
addPeakRegions |
should a merged set of peaks be created as one of the region sets (merged, non-overlapping peaks of width=500bp from the peaks of individual samples) |
sampleIdCol |
column name or index in the sample annotation table containing unique sample identifiers |
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. |
DsATAC
object
Fabian Mueller
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