arrayTrend: Spatial trend of microarray spots statistic

In MANOR: CGH Micro-Array NORmalization

Description

The function arrayTrend computes the spatial trend.

Usage

## Default S3 method:
arrayTrend(Statistic, Col, Row, ...)
## S3 method for class 'arrayCGH'
arrayTrend(arrayCGH, variable, ...)

Arguments

Statistic	Statistic to be smoothed.
Col	Vector of columns coordinates.
Row	Vector of rows coordinates.
arrayCGH	Object of class arrayCGH.
variable	Variable to be smooth.
...	Parameters to be passed to loess function.

Details

Spatial trend of microarray spots statistic.

Value

Either a data frame with elements :

Trend	Trend fitted by loess function.
Col	Vector of columns coordinates.
Row	Vector of rows coordinates.

or the element Trend is added to the data.frame arrayValues of the arrayCGH object.

Note

People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.

Author(s)

Philippe Hup?, [e-mail].

References

P. Neuvial, P. Hup?, I. Brito, S. Liva, E. Mani?, C. Brennetot, A. Aurias, F. Radvanyi, and E. Barillot. Spatial normalization of array-CGH data. BMC Bioinformatics, 7(1):264. May 2006.

See Also

loess, loess.control.

Examples

data(spatial)  ## arrays with local spatial effects

edgeTrend <- arrayTrend(edge, "LogRatio", span=0.03, degree=1,
iterations=3, family="symmetric") 
GLAD::arrayPlot(edgeTrend, "Trend", main="Spatial trend of array CGH", bar="v") 

MANOR documentation built on Nov. 8, 2020, 6:52 p.m.