Microarray database and utility functions for microarray data analysis.


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Documentation for package `maDB' version 1.8.0

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average Average signal channels of a microarray experiment
average,EexprSet-method Average signal channels of a microarray experiment
calculateSimilarity Calculate similarities (distances) between a vector and the rows (columns) of a matrix
checkForDifferentAnnotation Detect gene annotation differences
createDirs Create directories
createEexprSetFromLimma Changing a RGList or MAList into a object of the type EexprSet
createFile Create a file and all needed directories
createJOINQuery Create a SQL query that joins two or more tables
createNewDBTable Class "Sample"
createNewDBTable,Sample-method Class "Sample"
createNewDBTable,SignalChannel-method Micro array 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 the information about the comparisons from the database
dbGetExperimentInfo List information about an experiment from a database.
dbGetGeneRegulationRanking Rank genes according to the number of comparisons they are regulated.
dbSearchSimilarPattern Search for similar gene expression or regulation patterns in the database
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 method
distance.pearson.uncentered Calculate vector similarity (distance) using (uncentered) pearsons correlation method
distance.spearman Calculate spearmans rank correlation between two vectors
drawBioControls Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
drawBioControls,EexprSet-method Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
drawHistogram Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
drawHistogram,EexprSet-method Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
drawMA Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
drawMA,EexprSet-method Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
drawMA,exprSet-method Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
drawMAPlot Draw a standard MA plot
drawPolyAControls Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
drawPolyAControls,EexprSet-method Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
drawVolcanoPlot Draw a volcano plot
EexprSet Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
EexprSet-class Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
format.latex Formats strings to be LaTeX compliant
getA Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
getA,EexprSet-method Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
getAnnotation Annotate a gene
getArrays Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
getArrays,EexprSet-method Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
getContentMatrix Class "Sample"
getContentMatrix,Sample-method Class "Sample"
getContentMatrix,SignalChannel-method Micro array signal channel description
getData Class "Similarity"
getData,Similarity-method Class "Similarity"
getDistances Class "Similarity"
getDistances,Similarity-method Class "Similarity"
getEDB Retrieving expression values from a database.
getM Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
getM,EexprSet-method Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
getMDB Retrieving 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,Sample-method Class "Sample"
getSamplesFromDB Lists all or only specified samples from the database.
getSignalChannels Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
getSignalChannels,EexprSet-method Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
getWeights Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
getWeights,EexprSet-method Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
isDecimal Is the number a cardinal or a decimal number?
Layout-class Micro array grid and print tip layout description object
loadFromDB Load a Object from the database
loadFromDB,EexprSet-method Load a Object from the database
loadFromDB,Sample-method Load a Object from the database
loadFromDB-methods Load a Object from the database
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
NormChips example exprSet instance
plot,Similarity-method Class "Similarity"
plotSimilarity Draw a plot for the Similarity-class
print,Similarity-method Class "Similarity"
progress Progress bar
publishToDB Writing the expression values from normalized micro arrays into a database
publishToDB,EexprSet-method Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
replaceAll Replace all occurences of a specified character in a string by a new character
replaces Replace all occurences of a specified character in a string by a new character
Sample-class Class "Sample"
show,SignalChannel-method Micro array signal channel description
SignalChannel-class Micro array signal channel description
Similarity-class Class "Similarity"
sort,Similarity-method Class "Similarity"
toEexprSet Transfor objects to objects of the type EexprSet
toEexprSet,MAList-method Transfor objects to objects of the type EexprSet
toEexprSet,RGList-method Transfor objects to objects of the type EexprSet
toExprSet Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
toExprSet,EexprSet-method Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
writeFigure Includes a figure in a LaTeX document
writeLatexTable Writes a matrix or data frame in latex format to a file.
writeTable Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"
writeTable,EexprSet-method Class "EexprSet" an extended verision of the "exprSet" class from "Biobase"