cnSegmentation: Perform copy number segmentation

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Perform copy number segmentation

Description

Perform copy number segmentation using the signals in the signal set. The function takes a SigDF for the target sample and a set of normal SigDF for the normal samples. An optional arguments specifies the version of genome build that the inference will operate on. The function outputs an object of class CNSegment with signals for the segments ( seg.signals), the bin coordinates ( bin.coords) and bin signals (bin.signals).

Usage

cnSegmentation(
  sdf,
  sdfs.normal = NULL,
  genomeInfo = NULL,
  probeCoords = NULL,
  tilewidth = 50000,
  verbose = FALSE,
  return.probe.signals = FALSE
)

Arguments

sdf	SigDF
sdfs.normal	a list of SigDFs for normalization, if not given, use the stored normal data from sesameData. However, we do recommend using a matched copy number normal dataset for normalization. assembly
genomeInfo	the genomeInfo files. The default is retrieved from sesameData. Alternative genomeInfo files can be found at https://github.com/zhou-lab/GenomeInfo
probeCoords	the probe coordinates in the corresponding genome if NULL (default), then the default genome assembly is used. Default genome is given by, e.g., sesameData_check_genome(NULL, "EPIC") For additional mapping, download the GRanges object from http://zwdzwd.github.io/InfiniumAnnotation and provide the following argument ..., probeCoords = sesameAnno_buildManifestGRanges("downloaded_file"),... to this function.
tilewidth	tile width for smoothing
verbose	print more messages
return.probe.signals	return probe-level instead of bin-level signal

Value

an object of CNSegment

Examples

sesameDataCache()

## Not run: 
sdfs <- sesameDataGet('EPICv2.8.SigDF')
sdf <- sdfs[["K562_206909630040_R01C01"]]
seg <- cnSegmentation(sdf)
seg <- cnSegmentation(sdf, return.probe.signals=TRUE)
visualizeSegments(seg)

## End(Not run)

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.