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beadarray (version 2.22.2)

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

2.22.2

License

GPL-2

Maintainer

Last Published

February 15th, 2017

Functions in beadarray (2.22.2)

boxplot-methods

Boxplots from summary data

BASH - Extended Defect Analysis

beadarrayUsersGuide

View beadarray User's Guide

beadarray-package

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

Storage of annotation information

BASH - Compact Defect Analysis

BASH - Diffuse Defect Analysis

BASH - BeadArray Subversion of Harshlight

backgroundCorrectSingleSection

Background correct an array-section

controlProbeDetection

Percentage of beads detected

limmaResults-class

Class "limmaResults"

checkRegistration

Perform check for misregistered array segments.

BeadLevelList-class

Class "BeadLevelList"

calculateDetection

Calculate detection scores

Combine two objects.

calculateOutlierStats

Outlier distribution stats

illuminaChannel-class

Class "illuminaChannel"

beadRegistrationData-class

Class "beadRegistrationData"

ExpressionSetIllumina-class

Class "ExpressionSetIllumina"

convertBeadLevelList

Convert a BeadLevelList object into a beadLevelData object

GEO required fields

generateNeighbours

Generate matrix of neighbouring beads

expressionQCPipeline

Flexible bead-level QC pipeline

createTargetsFile

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

deprecatedFunctions

Deprecated Functions

makeGEOSubmissionFiles

Create files for a Gene Expression Omnibus submission

Get raw data from a beadLevelData object

Retrieve the dimensions of an object

HULK - Bead Array Normalization by NEighbourhood Residuals

Differential expression using limma

Retrieve control beads

identifyControlBeads

Classify each bead according to its control status

imageplot for beadLevelData object

illuminaOutlierMethod

Identifier outliers on an array section

Add, modify or remove data in a beadLevelData object

imageProcessing

Image processing functions

Tabulate QC scores

insertSectionData

Modify the sectionData slot

Function to construct the classic MA plots from a dataset

plotBeadLocations

Plot bead locations

Gets the number of beads from a beadLevelData object

Function to Plot the Layout of an Illumina BeadChip

Plot outlier locations

beadIntensityPlots

Plotting the intensities of selected beads on a section

Annotation definitions

noOutlierMethod

returns no outliers on an array section

medianNormalise

Median normalise data in a matrix

normaliseIllumina

Normalise Illumina expression data

metrics-methods

Accessing metrics information in bead-level objects

Read ``.locs'' file.

Read the Illumina tiff images

Set weights from BASH

Scatter plots and MA-plots for all specified arrays

Display object summary

Show Array Mask

Produce plots of the Illumina tiff images

squeezedVarOutlierMethod

Identifier outliers on an array section

Read BeadScan gene expression output

Read bead-level Illumina data

weightsOutlierMethod

returns all beads with weight=0.

Create summary values for specified IDs

readBeadSummaryData

Read BeadStudio gene expression output

readSampleSheet

Read a Sample sheet for a BeadArray experiment

Gets the section names from a beadLevelData Object

Plot the positive controls

Create a summarized object

processSwathData

Prepare iScan data for use with beadarray

transformFunctions

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