run_atac

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
)

Arguments

anaDir

analysis directory

input

Input object. Can be either NULL, a character string, a DsATAC. Set to NULL when you want to continue a previous analysis

sampleAnnot

sample annotation table (data.frame) or NULL if continuing existing analysis or input is a DsATAC object

genome

genome assembly. Only relevant if not continuing existing analysis and input is not a DsATAC object

sampleIdCol

column name in the sample annotation table containing unique sample Only relevant if not continuing existing analysis and input is not a DsATAC object

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 DsATAC object

startStage

stage where to start the analysis from. can be one of "raw", "filtered", "processed". Only relevant if not continuing existing analysis.

resetStage

flag indicating whether to reset the analysis directory (i.e. deleting previously generated reports and datasets), when continuing previous analyses (input argument is NULL).

Value

DsATAC object (invisible)

Author

Fabian Mueller