Add chromosome cytobands and chromosome arms to TapestriExperiment

getCytobands() retrieves the chromosome arm and cytoband for each probe based on stored positional data and saves them in rowData. This is run automatically as part of createTapestriExperiment(). Note: Some downstream smoothing and plotting functions may fail if chromosome arms are not present in rowData.

Usage

getCytobands(TapestriExperiment, genome = "hg19", verbose = TRUE)

Arguments

TapestriExperiment: TapestriExperiment object.
genome: Character, reference genome to use. Only hg19 is currently supported.
verbose: Logical, if TRUE (default), progress is output as message text.

Value

TapestriExperiment object with rowData updated to include chromosome arms and cytobands.

Examples

tap.object <- newTapestriExperimentExample() # example TapestriExperiment object
#> ℹ Moving gRNA probe  to `altExp` slot "grnaCounts".
#> ℹ Moving barcode probe  to `altExp` slot "barcodeCounts".
#> ℹ Moving chrY probe(s) probe_231, probe_232, probe_233, probe_234, probe_235, probe_236, probe_237, probe_238, probe_239, and probe_240 to `altExp` slot "chrYCounts".
tap.object <- getCytobands(tap.object, genome = "hg19")
#> ℹ Adding cytobands from hg19.