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beadarray (version 2.16.0)

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

2.16.0

License

GPL-2

Maintainer

Mark Dunning

Last Published

February 15th, 2017

Functions in beadarray (2.16.0)

BASH - BeadArray Subversion of Harshlight

controlProbeDetection

Percentage of beads detected

Combine two objects.

imageplot for beadLevelData object

imageProcessing

Image processing functions

Annotation definitions

beadIntensityPlots

Plotting the intensities of selected beads on a section

Read bead-level Illumina data

Read BeadScan gene expression output

BASH - Extended Defect Analysis

beadarray-package

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

Create a summarized object

transformFunctions

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

illuminaChannel-class

Class "illuminaChannel"

makeGEOSubmissionFiles

Create files for a Gene Expression Omnibus submission

limmaResults-class

Class "limmaResults"

GEO required fields

Add, modify or remove data in a beadLevelData object

insertSectionData

Modify the sectionData slot

Read ``.locs'' file.

Read the Illumina tiff images

BASH - Compact Defect Analysis

ExpressionSetIllumina-class

Class "ExpressionSetIllumina"

BASH - Diffuse Defect Analysis

Get raw data from a beadLevelData object

HULK - Bead Array Normalization by NEighbourhood Residuals

beadRegistrationData-class

Class "beadRegistrationData"

readSampleSheet

Read a Sample sheet for a BeadArray experiment

Gets the section names from a beadLevelData Object

Gets the number of beads from a beadLevelData object

Plot outlier locations

processSwathData

Prepare iScan data for use with beadarray

Plot the positive controls

backgroundCorrectSingleSection

Background correct an array-section

boxplot-methods

Boxplots from summary data

generateNeighbours

Generate matrix of neighbouring beads

beadarrayUsersGuide

View beadarray User's Guide

expressionQCPipeline

Flexible bead-level QC pipeline

identifyControlBeads

Classify each bead according to its control status

illuminaOutlierMethod

Identifier outliers on an array section

noOutlierMethod

returns no outliers on an array section

Storage of annotation information

calculateDetection

Calculate detection scores

calculateOutlierStats

Outlier distribution stats

deprecatedFunctions

Deprecated Functions

Retrieve the dimensions of an object

Differential expression using limma

Retrieve control beads

medianNormalise

Median normalise data in a matrix

metrics-methods

Accessing metrics information in bead-level objects

weightsOutlierMethod

returns all beads with weight=0.

Produce plots of the Illumina tiff images

Scatter plots and MA-plots for all specified arrays

normaliseIllumina

Normalise Illumina expression data

Show Array Mask

squeezedVarOutlierMethod

Identifier outliers on an array section

checkRegistration

Perform check for misregistered array segments.

BeadLevelList-class

Class "BeadLevelList"

createTargetsFile

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

convertBeadLevelList

Convert a BeadLevelList object into a beadLevelData object

Tabulate QC scores

Function to construct the classic MA plots from a dataset

plotBeadLocations

Plot bead locations

Function to Plot the Layout of an Illumina BeadChip

Set weights from BASH

Create summary values for specified IDs

Display object summary

readBeadSummaryData

Read BeadStudio gene expression output