smooth.CNA {DNAcopy} | R Documentation |

## Smooth a 'Copy Number Array' data object

### Description

Detect outliers and smooth the data prior to analysis by programs such
as circular binary segmentation (CBS).

### Usage

smooth.CNA(x, smooth.region=2, outlier.SD.scale=4, smooth.SD.scale=2,
trim=0.025)

### Arguments

`x` |
Copy number array data object |

`smooth.region` |
number of points to consider on the left and the
right of a point to detect it as an outlier. |

`outlier.SD.scale` |
the number of SDs away from the nearest point
in the smoothing region to call a point an outlier. |

`smooth.SD.scale` |
the number of SDs from the median in the
smoothing region where a smoothed point is positioned. |

`trim` |
proportion of data to be trimmed for variance calculation
for smoothing outliers and undoing splits based on SD. |

### Value

An object of class `CNA`

with outliers smoothed

### Examples

data(coriell)
#Combine into one CNA object to prepare for analysis on Chromosomes 1-23
CNA.object <- CNA(cbind(coriell$Coriell.05296,coriell$Coriell.13330),
coriell$Chromosome,coriell$Position,
data.type="logratio",sampleid=c("c05296","c13330"))
#We generally recommend smoothing single point outliers before analysis
#Make sure to check that the smoothing is proper
smoothed.CNA.object <- smooth.CNA(CNA.object)

[Package

*DNAcopy* version 1.1.0

Index]