makeQCTable {beadarray} | R Documentation

## Tabulate QC scores

### 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

    }

[Package beadarray version 2.37.1 Index]