callXXorXY.numeric: Calls XX or XY from ChrX allele B fractions of a normal...

In HenrikBengtsson/aroma.cn: Copy-Number Analysis of Large Microarray Data Sets

Calls XX or XY from ChrX allele B fractions of a normal sample

Description

Calls XX or XY from ChrX allele B fractions of a normal sample.

Usage

## S3 method for class 'numeric'
callXXorXY(betaX, betaY=NULL, flavor=c("density"), adjust=1.5, ...,
  censorAt=c(-0.5, +1.5), verbose=FALSE)

Arguments

betaX	A numeric vector containing ChrX allele B fractions.
betaY	A optional numeric vector containing ChrY allele B fractions.
flavor	A character string specifying the type of algorithm used.
adjust	A postive double specifying the amount smoothing for the empirical density estimator.
...	Additional arguments passed to findPeaksAndValleys.
censorAt	A double vector of length two specifying the range for which values are considered finite. Values below (above) this range are treated as -Inf (+Inf).
verbose	A logical or a Verbose object.

Value

Returns a ...

Missing and non-finite values

Missing and non-finite values are dropped before trying to call XX or XY.

Author(s)

Henrik Bengtsson, Pierre Neuvial

See Also

Internally findPeaksAndValleys is used to identify the thresholds.

HenrikBengtsson/aroma.cn documentation built on Feb. 20, 2024, 9:15 p.m.