WACA: Waves aCGH Correction Algorithm

In cghRA: Array CGH Data Analysis and Visualization

Description

This function applies the Waves aCGH Correction Algorithm to a series a logRatio (usually a complete series of probe logRatio from a single CGH array), using the probe-dependant biases computed by the bias function.

Usage

  WACA(probeNames, probeLogRatios, bias, forceBiasOrdering = TRUE)

Arguments

probeNames	Character vector, the names of the probes to correct. All these names should be present in bias row.names.
probeLogRatios	Numeric vector, the logRatios of the probes to correct.
bias	A data.frame, as returned by the bias function.
forceBiasOrdering	Single logical value, whether to force the bias data.frame ordering / subsetting / replication or not. bias must be ordered according to probeNames (that can contain duplicates), if they are not the former needs to be reordered. If they have different lengths, ordering is forced. If not, it is up to the user to assure they are or to set forceBiasOrdering to TRUE (the default value). It might be time-saving to order bias manually and set this parameter to FALSE when applying WACA on several arrays from the same design.

Value

Returns a numeric vector with the corrected logRatios, preserving the probeNames and probeLogRatios order.

Author(s)

Sylvain Mareschal

References

Lepretre F. et al. (2010) Waved aCGH: to smooth or not to smooth. Nucleic Acids Res. 2010 Apr;38(7):e94

See Also

bias

cghRA documentation built on May 2, 2019, 3:34 a.m.