DsATAC.snakeATAC | R Documentation |
Create a DsATAC dataset from multiple input files output by snakeATAC
DsATAC.snakeATAC(
sampleAnnot,
filePrefixCol,
genome,
dataDir = "",
regionSets = NULL,
sampleIdCol = filePrefixCol,
type = "insBam",
diskDump = FALSE,
keepInsertionInfo = TRUE,
bySample = FALSE,
pairedEnd = TRUE
)
sampleAnnot |
data.frame specifying the sample annotation table |
filePrefixCol |
column name specifying the file prefix for each sample in the sample annotation table. If |
genome |
genome assembly |
dataDir |
directory where the files are located. If it is the empty character ( |
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 |
type |
input data type. Currently only "insBed" (insertion beds), "insBam" (insertion info inferred from bam files (aligned reads); default) and "bam" (aligned reads) are supported |
diskDump |
should large data objects (count matrices, fragment data, ...) be disk-backed to save main memory |
keepInsertionInfo |
flag indicating whether to maintain the insertion information in the resulting object. Only relevant when |
bySample |
process sample-by-sample to save memory (currently only has an effect for |
pairedEnd |
is the input data paired-end? Only relevant when |
DsATAC
object
Fabian Mueller
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