maDB-package |
Package to store and retrieve microarray experiments into/from a database. |
arrowProgress |
Progress bar with an arrow |
average |
Average signal channels of a microarray experiment |
average,MadbSet-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 |
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 |
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 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 |
drawHistogram |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
drawHistogram,MadbSet-method |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
drawMA |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
drawMA,ExpressionSet-method |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
drawMA,MadbSet-method |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
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 "Biobase" |
getA,MadbSet-method |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getAnnotation |
Annotate a gene |
getArrays |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getArrays,MadbSet-method |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getContentMatrix |
Class "Sample" |
getContentMatrix,Sample-method |
Class "Sample" |
getContentMatrix,SignalChannel-method |
Microarray 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 "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getM,MadbSet-method |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
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,Sample-method |
Class "Sample" |
getSamplesFromDB |
Lists all or only specified samples from the database. |
getSignalChannels |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getSignalChannels,MadbSet-method |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getWeights |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
getWeights,MadbSet-method |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
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,MadbSet-method |
Load a dataset from the database |
loadFromDB,Sample-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 database. |
MadbSet |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
MadbSet-class |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |
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,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,MadbSet-method |
Class "MadbSet" an extended version of the "ExpressionSet" 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 "Sample" |
Sample-class |
Class "Sample" |
show,SignalChannel-method |
Microarray signal channel description |
SignalChannel-class |
Microarray signal channel description |
Similarity-class |
Class "Similarity" |
sort,Similarity-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 "Biobase" |
writeTable,MadbSet-method |
Class "MadbSet" an extended version of the "ExpressionSet" class from "Biobase" |