run_atac | R Documentation |
Run the complete ChrAccR analysis for ATAC-seq data
run_atac(
anaDir,
input = NULL,
sampleAnnot = NULL,
genome = NULL,
sampleIdCol = NULL,
regionSets = NULL,
startStage = "raw",
resetStage = NULL
)
anaDir |
analysis directory |
input |
Input object. Can be either |
sampleAnnot |
sample annotation table ( |
genome |
genome assembly. Only relevant if not continuing existing analysis and input is not a |
sampleIdCol |
column name in the sample annotation table containing unique sample Only relevant if not continuing existing analysis and input is not a |
regionSets |
a list of GRanges objects which contain region sets over which count data will be aggregated. Only relevant if not continuing existing analysis and input is not a |
startStage |
stage where to start the analysis from. can be one of |
resetStage |
flag indicating whether to reset the analysis directory (i.e. deleting previously generated reports and datasets), when continuing previous analyses ( |
DsATAC
object (invisible)
Fabian Mueller
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