qcBeadLevel {beadarray} | R Documentation

## Generate simple diagnostic plots for Illumina bead-level data

### Description

Generate simple diagnostic plots for Illumina bead-level data

### Usage

    qcBeadLevel(object, whatToPlot="G", RG=FALSE, log=TRUE, nrow = 100, ncol= 100,
                        colDens=1, colBox=0, html=TRUE,
                        fileName="qcsummary.htm", plotdir=NULL,
                        experimentName=NULL, targets=NULL, ...)

### Arguments

`object` | `BeadLevelList`
`whatToPlot` | character string or vector specifying which intensities to plot. Possibilities are `"G"`, `"Gb"` for single channel data and `"G"`, `"Gb"`, `"R"`, `"Rb"` and `"M"` for two-colour data
`RG` | if TRUE, plot R vs G intensities per array. Default value is FALSE. Only useful for two-channel data
`log` | if TRUE log2 intensities are plotted
`nrow` | integer specifying the number of rows to divide the image into (used by `imageplot` function)
`ncol` | integer specifying the number of columns to divide the image into (used by `imageplot`)
`colDens` | colours for density plots (default is 1)
`colBox` | colours for box plot (default is 0)
`html` | logical scalar. If `TRUE` an html summary page is generated. If `FALSE`, no summary page is generated.
`fileName` | name of html summary page. Default is `"qcsummary.htm"`.
`plotdir` | optional character string specifying the filepath where the plots will be saved. Defaults to the current working directory.
`experimentName` | name to appear on HTML report (default is NULL).
`targets` | `data.frame` containing sample information
`...` | further arguments that can be passed to the plotting functions.

### Details

This function creates boxplots, smoothed histogram (density) plots and imageplots of raw bead-level intensity data.

An html page which displays the results, is created when `html=TRUE`. The html page name is specified by the `fileName` argument.

### Author(s)

Matt Ritchie

### Examples

    #data(BLData)
    #qcBeadLevel(BLData)

[Package beadarray version 1.10.0 Index]