makeQCTable: Tabulate QC scores

In markdunning/beadarray-devel: Quality assessment and low-level analysis for Illumina BeadArray data

Description

Function to make a table of quality control scores for every section in a beadLevelData object. Either the annotation of the data needs to be specified, or a control profile data frame that lists ArrayAddress IDs and control types. The supplied summary functions are applied to each control type on each section.

Usage

makeQCTable(BLData, transFun = logGreenChannelTransform, controlProfile = NULL, summaryFns = list(Mean = function(x) mean(x, na.rm=TRUE), Sd = function(x) sd(x, na.rm=TRUE)), channelSuffix = NULL)

Arguments

BLData	a beadLevelData object
transFun	a function to be applied to the beadLevelData object prior to tabulation
controlProfile	an optional data frame that specifies ID and type of controls to be used to generate the table
summaryFns	list of functions to apply to each control type on every section
channelSuffix	optional character string to append to the column names of the resulting table

Details

For each section in turn, the function groups together IDs of the same control type (e.g. housekeeping), and uses an lapply with the specified summary functions. A transformation function is applied to BLData prior to the summary, with the default being to take the log2 of the green channel.

If the annotation of the beadLevelData has been set by readIllumina or setAnnotation then the controlProfile data frame is calculated automatically and the controlProfile argument may be omitted.

Value

A matrix with one row per section and one column for each combination of control type and summary function.

Author(s)

Mark Dunning

Examples

if(require(beadarrayExampleData)){

data(exampleBLData)


qct = makeQCTable(exampleBLData)

qct

}

markdunning/beadarray-devel documentation built on May 21, 2019, noon