arrowProgress |
Progress bar with an arrow |
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" |
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" |