DsATAC.snakeATAC.RdCreate 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
)data.frame specifying the sample annotation table
column name specifying the file prefix for each sample in the sample annotation table. If dataDir is not empty (i.e. not "")
filenames are assumed to be relative to that directory and a corresponding filename suffix will be appended
genome assembly
directory where the files are located. If it is the empty character (""; default) it is assumed that filePrefixCol specifies the full path to the input files
a list of GRanges objects which contain region sets over which count data will be aggregated
column name or index in the sample annotation table containing unique sample identifiers
input data type. Currently only "insBed" (insertion beds), "insBam" (insertion info inferred from bam files (aligned reads); default) and "bam" (aligned reads) are supported
should large data objects (count matrices, fragment data, ...) be disk-backed to save main memory
flag indicating whether to maintain the insertion information in the resulting object. Only relevant when type=="insBam".
process sample-by-sample to save memory (currently only has an effect for type=="insBam")
is the input data paired-end? Only relevant when type=="insBam".
DsATAC object