modulefunctions: Functions for computing quality report modules.

Description

These functions produce objects of class aqmReportModule representing the various modules of the quality report. Given a list of modules, the report is then rendered by the aqm.writereport function.

Most users will not call these functions directly, but will use the function arrayQualityMetrics, which in turns calls these functions. The function arguments can be provided through the ... argument of arrayQualityMetrics.

Usage

aqm.boxplot(x, subsample=20000, outlierMethod = "KS", ...)
aqm.density(x, ...)
aqm.heatmap(x, ...)
aqm.pca(x, ...)
aqm.maplot(x, subsample=20000, Dthresh=0.15, maxNumArrays=8, nrColumns=4, ...)
aqm.spatial(x, scale="rank", channels = c("M", "R", "G"), maxNumArrays=8, nrColumns=4, ...)
aqm.meansd(x, ...)
aqm.probesmap(x, ...)
# Affymetrix specific sectionsaqm.pmmm(x, ...)
aqm.rnadeg(expressionset, x, ...)
aqm.rle(x, outlierMethod = "KS", ...)
aqm.nuse(x, outlierMethod = "upperquartile", ...)

Arguments

An object resulting from a call to prepdata(expressionset).

expressionset

An object of class AffyBatch.

subsample

For efficiency, some computations are performed not on the full set of features (which can be hundreds of thousands on some arrays), but on a randomly subset whose size is indicated by this number.

outlierMethod

As in outliers.

Dthresh

In maplot, the arrays with a Hoeffding D statistic larger than this value are called outliers. See also hoeffd.

scale, channels

In aqm.spatial, scale determines the choice of the false colour scale in the spatial plots. If the value is "rank", then the colour is proportional to the ranks of the values; if it is "direct", then it is proportional to the values themselves. channels determines for which elements of x spatial plots are made.

maxNumArrays, nrColumns

The parameter maxNumArrays determines the number of arrays for which a plot is produced. nrColumns determines the number of columns in the multi-panel plot. In aqm.maplot, first maxNumArrays is incremented to the next multiple of maxNumArrays. A value of +Inf is allowed. If this value is larger than or equal to the actual number of arrays in x, then plots are produced for all arrays. If it is smaller, then plots are shown for the maxNumArrays/2 with the worst values of Hoeffding's D and for the maxNumArrays/2 best.

...

Will be ignored - the dots are formal arguments which permit that all of these functions can be callled from arrayQualityMetrics with the same, overall set of arguments.

Value

An object of class aqmReportModule.

Details

For a simple example of the aqm.* functions, have a look at the source code of the aqm.pca function. Please see also the vignette Advanced topics: Customizing arrayQualityMetrics reports and programmatic processing of the output.