Microarray database and utility functions for microarray data analysis.


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Documentation for package ‘maDB’ version 1.22.0

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maDB-package Package to store and retrieve microarray experiments into/from a
arrowProgress Progress bar with an arrow
average Average signal channels of a microarray experiment
average-method Average signal channels of a microarray experiment
calculateSimilarity Calculate similarities (distances) between a vector and the rows
checkForDifferentAnnotation Detect gene annotation differences
createDirs Create directories
createFile Create a file and all needed directories
createJOINQuery Create a SQL query that joins two or more tables
createNewDBTable Class "Sample"
createNewDBTable-method Class "Sample"
createNewDBTable-method Microarray signal channel description
createSampleFromTable Create a new Sample object using data from a matrix
dbCalculateRegulations Calculate regulation values from expression values in the database
dbGetAnnotation Annotate a list of IDs using the annotation table in the database.
dbGetComparisons Get a list of all comparisons from the database
dbGetExperimentInfo List information about an experiment from the database.
dbGetGeneRegulationRanking Rank genes according to the number of comparisons they are regulated.
dbSearchSimilarPattern Search for similar gene expression or regulation patterns in the
dbUpdateAnnotation Create and update an annotation table in a PostgreSQL database.
deleteExperimentFromDB Deleting a experiment from a database.
distance.euclidian Calculate vector similarity (distance) using euclidian distance metrics
distance.pearson Calculate vector similarity (distance) using pearsons correlation
distance.pearson.uncentered Calculate vector similarity (distance) using (uncentered) pearsons
distance.spearman Calculate spearmans rank correlation between two vectors
drawHistogram Class "MadbSet" an extended version of the "ExpressionSet" class from
drawHistogram-method Class "MadbSet" an extended version of the "ExpressionSet" class from
drawMA Class "MadbSet" an extended version of the "ExpressionSet" class from
drawMA-method Class "MadbSet" an extended version of the "ExpressionSet" class from
drawMAPlot Draw a standard MA plot
drawVolcanoPlot Draw a volcano plot
format.latex Formats strings
getA Class "MadbSet" an extended version of the "ExpressionSet" class from
getA-method Class "MadbSet" an extended version of the "ExpressionSet" class from
getAnnotation Annotate a gene
getArrays Class "MadbSet" an extended version of the "ExpressionSet" class from
getArrays-method Class "MadbSet" an extended version of the "ExpressionSet" class from
getContentMatrix Class "Sample"
getContentMatrix-method Class "Sample"
getContentMatrix-method Microarray signal channel description
getData Class "Similarity"
getData-method Class "Similarity"
getDistances Class "Similarity"
getDistances-method Class "Similarity"
getEDB Retrieving expression values from a database.
getM Class "MadbSet" an extended version of the "ExpressionSet" class from
getM-method Class "MadbSet" an extended version of the "ExpressionSet" class from
getMDB Retriev regulation values from a database.
getPathFromFile Get the path to a file
getPK Getting the primary key of the appropriate object from the database
getPK-method Class "Sample"
getSamplesFromDB Lists all or only specified samples from the database.
getSignalChannels Class "MadbSet" an extended version of the "ExpressionSet" class from
getSignalChannels-method Class "MadbSet" an extended version of the "ExpressionSet" class from
getWeights Class "MadbSet" an extended version of the "ExpressionSet" class from
getWeights-method Class "MadbSet" an extended version of the "ExpressionSet" class from
isDecimal Is the number a cardinal or a decimal number?
Layout-class Microarray grid and print tip layout description object
loadFromDB Load a dataset from the database
loadFromDB-method Load a dataset from the database
loadFromDB-methods Load a dataset from the database
maDB Package to store and retrieve microarray experiments into/from a
MadbSet Class "MadbSet" an extended version of the "ExpressionSet" class from
MadbSet-class Class "MadbSet" an extended version of the "ExpressionSet" class from
MAtoG Calculate the green intensity values from the M and A values given.
MAtoR Calculate the red intensity values from the M and A values given.
mean.center Mean center a numerical vector
meanWithoutNA Calculating the mean by excluding all NA and NULL values
medianWithoutNA Calculating the median by excluding all NA and NULL values
multiapply Apply a function to two arrays
multiGrep Perform a pattern search with a list of patterns
myGrep Perform a pattern search
newMadbSet Create a new MadbSet object
NormChips example exprSet instance
openMadbVignette maDB vignette
plot-method Class "Similarity"
plotSimilarity Draw a plot for the Similarity-class
print-method Class "Similarity"
progress Progress bar
publishToDB Writing the expression values from normalized micro arrays into a
publishToDB-method Class "MadbSet" an extended version of the "ExpressionSet" class from
replaceAll Replace all occurences of a specified character in a string by a new
replaces Replace all occurences of a specified character in a string by a new
Sample Class "Sample"
Sample-class Class "Sample"
show-method Microarray signal channel description
SignalChannel-class Microarray signal channel description
Similarity-class Class "Similarity"
sort-method Class "Similarity"
writeFigure Includes a figure in a LaTeX document
writeLatexTable Writes a matrix or data frame in latex format to a file.
writeTable Class "MadbSet" an extended version of the "ExpressionSet" class from
writeTable-method Class "MadbSet" an extended version of the "ExpressionSet" class from