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

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Description

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

Usage

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## 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.

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