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beadarray (version 2.18.0)

Quality assessment and low-level analysis for Illumina BeadArray data

Description

The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

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Version

Version

2.18.0

License

GPL-2

Maintainer

Mark Dunning

Last Published

February 15th, 2017

Functions in beadarray (2.18.0)

BASH - Compact Defect Analysis

boxplot-methods

Boxplots from summary data

Storage of annotation information

beadarrayUsersGuide

View beadarray User's Guide

backgroundCorrectSingleSection

Background correct an array-section

BASH - Diffuse Defect Analysis

beadarray-package

The beadarray package: a tool for low-level analysis of Illumina BeadArrays

BASH - Extended Defect Analysis

BASH - BeadArray Subversion of Harshlight

calculateOutlierStats

Outlier distribution stats

calculateDetection

Calculate detection scores

convertBeadLevelList

Convert a BeadLevelList object into a beadLevelData object

createTargetsFile

A function to generate a targets file given a directory of Illumina bead-level files

Tabulate QC scores

Combine two objects.

controlProbeDetection

Percentage of beads detected

deprecatedFunctions

Deprecated Functions

Retrieve the dimensions of an object

beadRegistrationData-class

Class "beadRegistrationData"

Get raw data from a beadLevelData object

ExpressionSetIllumina-class

Class "ExpressionSetIllumina"

HULK - Bead Array Normalization by NEighbourhood Residuals

Retrieve control beads

Differential expression using limma

Gets the number of beads from a beadLevelData object

Plot outlier locations

Read ``.locs'' file.

Read the Illumina tiff images

weightsOutlierMethod

returns all beads with weight=0.

Annotation definitions

Function to construct the classic MA plots from a dataset

beadIntensityPlots

Plotting the intensities of selected beads on a section

Read BeadScan gene expression output

Read bead-level Illumina data

checkRegistration

Perform check for misregistered array segments.

BeadLevelList-class

Class "BeadLevelList"

makeGEOSubmissionFiles

Create files for a Gene Expression Omnibus submission

GEO required fields

Show Array Mask

metrics-methods

Accessing metrics information in bead-level objects

medianNormalise

Median normalise data in a matrix

identifyControlBeads

Classify each bead according to its control status

illuminaOutlierMethod

Identifier outliers on an array section

Plot the positive controls

processSwathData

Prepare iScan data for use with beadarray

Set weights from BASH

Display object summary

limmaResults-class

Class "limmaResults"

illuminaChannel-class

Class "illuminaChannel"

plotBeadLocations

Plot bead locations

imageProcessing

Image processing functions

imageplot for beadLevelData object

Function to Plot the Layout of an Illumina BeadChip

Scatter plots and MA-plots for all specified arrays

Produce plots of the Illumina tiff images

expressionQCPipeline

Flexible bead-level QC pipeline

Add, modify or remove data in a beadLevelData object

generateNeighbours

Generate matrix of neighbouring beads

insertSectionData

Modify the sectionData slot

noOutlierMethod

returns no outliers on an array section

Create summary values for specified IDs

normaliseIllumina

Normalise Illumina expression data

readBeadSummaryData

Read BeadStudio gene expression output

readSampleSheet

Read a Sample sheet for a BeadArray experiment

Gets the section names from a beadLevelData Object

Create a summarized object

squeezedVarOutlierMethod

Identifier outliers on an array section

transformFunctions

Functions for transforming the data store in a beadLevelData object for easier visualisation or summarisation.