lumi (version 2.24.0)

monoSmu: Monotonic smooth method

Description

Fit the monotonic-constraint spline curve

Usage

monoSmu(x, y, newX = NULL, nSupport = min(200, length(x)), nKnots = 6, rotate = FALSE, ifPlot = FALSE, xlab = 'x', ylab = 'y', ...)

Arguments

x

a vector represents x values

y

a vector represents y values

newX

the new values to be transformed. If not provided, "x" will be used.

nSupport

downsampled data points

nKnots

parameter used by monoSpline

rotate

determine whether to rotate the axis with 45 degrees in clockwise, i.e., fit the curve in the MA-plot.

ifPlot

determine whether to plot intermediate results

xlab

the xlab of the plot

ylab

the ylab of the plot

...

parameters used by supsmu and plot

Value

Return the transformed "newX" based on the smoothed curve

Details

function called by lumiN.rsn. The function first fits a monotonic spline between vector x and y, then transforms the vector newX based on the fitted spline. (After transformation the fitted spline is supposed to be a diagonal line, i.e., x=y)

References

Lin, S.M., Du, P., Kibbe, W.A., (2008) 'Model-based Variance-stabilizing Transformation for Illumina Microarray Data', Nucleic Acids Res. 36, e11

See Also

monoSpline