getCytobands: Add chromosome cytobands and chromosome arms to...

In karyotapR: DNA Copy Number Analysis for Genome-Wide Tapestri Panels

Add chromosome cytobands and chromosome arms to TapestriExperiment

Description

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
tap.object <- getCytobands(tap.object, genome = "hg19")

karyotapR documentation built on Sept. 8, 2023, 5:07 p.m.