Learn R Programming

⚠️There's a newer version (2.22.2) of this package.Take me there.

beadarray (version 2.20.0)

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.

Copy Link

Version

Version

2.20.0

License

GPL-2

Maintainer

Mark Dunning

Last Published

February 15th, 2017

Functions in beadarray (2.20.0)

Storage of annotation information

boxplot-methods

Boxplots from summary data

BASH - Extended Defect Analysis

beadarrayUsersGuide

View beadarray User's Guide

backgroundCorrectSingleSection

Background correct an array-section

BASH - BeadArray Subversion of Harshlight

BASH - Compact Defect Analysis

BASH - Diffuse Defect Analysis

beadarray-package

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

beadRegistrationData-class

Class "beadRegistrationData"

limmaResults-class

Class "limmaResults"

ExpressionSetIllumina-class

Class "ExpressionSetIllumina"

checkRegistration

Perform check for misregistered array segments.

illuminaChannel-class

Class "illuminaChannel"

BeadLevelList-class

Class "BeadLevelList"

calculateDetection

Calculate detection scores

calculateOutlierStats

Outlier distribution stats

Combine two objects.

controlProbeDetection

Percentage of beads detected

generateNeighbours

Generate matrix of neighbouring beads

makeGEOSubmissionFiles

Create files for a Gene Expression Omnibus submission

convertBeadLevelList

Convert a BeadLevelList object into a beadLevelData object

expressionQCPipeline

Flexible bead-level QC pipeline

GEO required fields

Retrieve the dimensions of an object

deprecatedFunctions

Deprecated Functions

HULK - Bead Array Normalization by NEighbourhood Residuals

Get raw data from a beadLevelData object

createTargetsFile

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

illuminaOutlierMethod

Identifier outliers on an array section

identifyControlBeads

Classify each bead according to its control status

insertSectionData

Modify the sectionData slot

Differential expression using limma

Add, modify or remove data in a beadLevelData object

Tabulate QC scores

Function to construct the classic MA plots from a dataset

imageplot for beadLevelData object

imageProcessing

Image processing functions

Retrieve control beads

noOutlierMethod

returns no outliers on an array section

normaliseIllumina

Normalise Illumina expression data

Plot outlier locations

medianNormalise

Median normalise data in a matrix

Function to Plot the Layout of an Illumina BeadChip

Annotation definitions

metrics-methods

Accessing metrics information in bead-level objects

beadIntensityPlots

Plotting the intensities of selected beads on a section

Gets the number of beads from a beadLevelData object

plotBeadLocations

Plot bead locations

Scatter plots and MA-plots for all specified arrays

Plot the positive controls

Read the Illumina tiff images

processSwathData

Prepare iScan data for use with beadarray

Read bead-level Illumina data

Read BeadScan gene expression output

Read ``.locs'' file.

Produce plots of the Illumina tiff images

readBeadSummaryData

Read BeadStudio gene expression output

Create a summarized object

transformFunctions

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

Set weights from BASH

Display object summary

squeezedVarOutlierMethod

Identifier outliers on an array section

weightsOutlierMethod

returns all beads with weight=0.

Show Array Mask

readSampleSheet

Read a Sample sheet for a BeadArray experiment

Gets the section names from a beadLevelData Object

Create summary values for specified IDs