smooth.CNA {DNAcopy} | R Documentation |
Detect outliers and smooth the data prior to analysis by programs such as circular binary segmentation (CBS).
smooth.CNA(x, smooth.region=2, outlier.SD.scale=4, smooth.SD.scale=2, trim=0.025)
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. |
An object of class CNA
with outliers smoothed
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)