Smooth copy number values across chromosomes and chromosome arms

calcSmoothCopyNumber() takes copyNumber slot values for probes on a chromosome and smooths them by median (default) for each chromosome and chromosome arm, resulting in one copy number value per chromosome and chromosome arm for each cell barcode. Cell-chromosome values are then discretized into integers by conventional rounding (1.5 <= x < 2.5 rounds to 2). Smoothed copy number and discretized smoothed copy number values are stored as smoothedCopyNumber and discreteCopyNumber assays, in altExp slots smoothedCopyNumberByChr for chromosome-level smoothing, and smoothedCopyNumberByArm for chromosome arm-level smoothing.

Usage

calcSmoothCopyNumber(TapestriExperiment, method = "median")

Arguments

TapestriExperiment: TapestriExperiment object.
method: Character, smoothing method: median (default) or mean.

Value

TapestriExperiment with smoothedCopyNumber and discreteCopyNumber assays in altExp slots smoothedCopyNumberByChr and smoothedCopyNumberByArm.

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 <- calcNormCounts(tap.object)
control.copy.number <- generateControlCopyNumberTemplate(tap.object,
  copy.number = 2,
  sample.feature.label = "cellline1"
)
tap.object <- calcCopyNumber(tap.object,
  control.copy.number,
  sample.feature = "test.cluster"
)
tap.object <- calcSmoothCopyNumber(tap.object)
#> ℹ Smoothing copy number by median...
#> ✔ Smoothing copy number by median... [918ms]
#>