Man pages for HenrikBengtsson/aroma
An R Object-oriented Microarray Analysis package

AcceptFilterThe AcceptFilter class
addFlag.MicroarrayDataFlags or unflags the indices of some spots with a specific...
AffineModelFitModel fit of affine microarray models
AFilterFieldFilter for the log-intensities (A)
AndFilterThe AndFilter class
append.MicroarrayDataAppends another MicroarrayData object
aroma-packagePackage aroma
as.character.SpotPositionGets a character represenation of the spot positions
as.data.frame.MicroarrayDataConverts the object to a data frame
as.data.frame.SpotPositionGets a data frame represenation of the spot positions
as.layout.SMAConverts a aroma object into an object of the layout...
as.MAData.RGDataTransform from the red and green intensities into log ratios...
as.RGData.MADataTransform MA format into RG format
as.RG.SMAConverts a aroma object into an object of the RG structure
boxplot.MicroarrayDataPlots a boxplot
calibrateMultiscan.RGDataCalibrates multiple re-scanned images based on an affine...
changeInput.FilterChange input(s) on this filter and optionally all filters...
changeInput.ParallelFilterReplaces input filters with other ones
changeInput.SerialFilterChange input(s) on this filter and optionally all filters...
clearFlag.MicroarrayDataClears the spots from the specified flag
convertFieldNames.GenePixDataConvert field names that contains patterns
DfFilterFieldFilter for the log-intensities (A)
equals.LayoutChecks if a Layout object is equals to some other object
equals.MicroarrayDataCompares a MicroarrayData object with another Object
estimateMACurve.MADataEstimates a smooth intensity-dependent curve in (A,M)
ExperimentalSetupThe ExperimentalSetup class
extract.MicroarrayDataGets a subset of data specified by fields, slides and/or spot...
FieldFilterThe FieldFilter class
FilterThe Filter class
findSetupFiles.ExperimentalSetupLocates cDNA microarray experiment setup files
fitMultiscanAffine.RGDataFits an affine model to signals from a multi-scanned slide
fromSaturatedSignals.SignalWeightsWeight function for scanner signals
GalLayoutClass representing GenePix Array List (GAL) data
GeneAcceptFilterThe GeneAcceptFilter class
GeneGroupsThe GeneGroups class
GenePixDataThe GenePixData class
GeneRejectFilterThe GeneRejectFilter class
getAdjustedSpotVariability.MADataGets the spotwise intensity-adjusted variability of replicate...
getArea.GenePixDataGets the area of the spot
getAspectRatio.SpotPositionGets the aspect ratio of the spots
getBackground.RawDataGets the background signal
getBackgroundSD.GenePixDataGets the standard deviation of the background pixels
getBottomEdge.SpotPositionGets the y-coordinate of the spot at the very bottom
getChannelNames.GenePixDataGets the names of the channels
getChannelNames.MicroarrayDataGets the names of the channels
getColors.MADataGenerates colors for each of the specified spots
getColors.RawDataGenerates colors for each of the specified spots
getColors.RGDataGenerates red to green colors for each of the specified spots
getDistancesTo.SpotPositionGets the Euclidean distance from one spot to a set of other...
getDuplicates.GeneGroupsGets all duplicated spots
getExtra.MicroarrayDataGets an extra field
getFieldNames.MicroarrayDataGets the names of all fields containing spot specific data
getFlag.MicroarrayDataGets the indices of the spots flagged with a specific flag
getForeground.RawDataGets the foreground signal
getForegroundSD.GenePixDataGets the standard deviation of the foreground pixels
getForegroundSD.SpotDataGets (an approximation of) the standard deviation of the...
getForegroundSE.GenePixDataGets the standard error of the foreground pixels
getForegroundSE.SpotDataGets the standard error of the foreground pixels
getGeneSlideReplicateIndex.MicroarrayDataReturns the index of the spots in (gene,slide,replicate)...
getGeneVariability.MADataGets the genewise variability
getId.LayoutGets the id of one or more spots
getIndex.AcceptFilterGets indices accepted by this filter
getIndex.AndFilterGets indices accepted by this filter
getIndex.FieldFilterGets indices accepted by this filter
getIndex.FilterGets the indices accepted by the filter
getIndex.LayoutGets the index of a spot given its location
getIndex.OrFilterGets indices accepted by this filter
getIndices.LayoutGets the indices of the spots at the given locations
getInput.FilterGets all the input objects connected to the filter
getInput.ParallelFilterGets the input filters
getInput.SerialFilterGets all the input objects connected to the filter
getLabel.MicroarrayDataGets the label of one field
getLayout.MicroarrayDataGets the layout
getLeftEdge.SpotPositionGets the x-coordinate of the left most spot
getLocation.LayoutGets the location of a spot given its index
getLogIntensities.RGDataCalculates the log-intensitites (A values)
getLogRatios.RGDataCalculates the log-ratios (M values)
getMaxHeight.SpotPositionGets the maximum y-distance between two spots
getMaxWidth.SpotPositionGets the maximum x-distance between two spots
getMOR2003a.MADataGets the Intensity Adjusted Measure of Reproducibility
getMOR.MADataGets the Measure of Reproducibility
getName.LayoutGets the name of one or more spots
getNames.GeneGroupsGets the names of the unique gene names
getParameter.FilterGets the values for a specific parameter for indices accepted...
getPosition.LayoutGets the position of a set of spots given their indices
getPrintorder.LayoutGets the order of the spots in which they were printed
getQuadruplicates.GeneGroupsGets all quadruplicated spots
getRawData.GenePixDataGets the raw intensites from the GPR structure
getRawData.ImaGeneDataGets the raw intensites from two ImaGeneData objects
getRawData.QuantArrayDataGets the raw intensites from the QuantArray data structure
getRawData.ScanAlyzeDataGets the raw (foreground and background) intensites
getRawData.SpotDataGets the raw intensites from the SpotData structure
getRawData.SpotfinderDataGets the raw intensites from the SpotfinderData structure
getReplicates.GeneGroupsGets all spots that exist with a certain number of replicates
getRightEdge.SpotPositionGets the x-coordinate of the right most spot
getSignal.RawDataGets the red and the green signal
getSizes.GeneGroupsGets the number of replicates for each gene
getSlideNames.MicroarrayDataGets the names of the slides
getSpotPosition.GenePixDataGets physical positions of the spots
getSpotPosition.ImaGeneDataGets physical positions of the spots
getSpotPosition.QuantArrayDataGets physical positions of the spots
getSpotPosition.ScanAlyze20DataGets physical positions of the spots
getSpotPosition.ScanAlyzeDataGets physical positions of the spots
getSpotPosition.SpotDataGets physical positions of the spots
getSpots.GeneGroupsGets a list of items each containing spot indices for a group
getTopEdge.SpotPositionGets the y-coordinate of the spot at the very top
getTriplicates.GeneGroupsGets all triplicated spots
getVisible.FilterChecks if the filter is visible or not
gridSize.LayoutGets the number of spots in each grid
hasLayout.MicroarrayDataChecks if the layout has been specified
highlight.FilterHighlights the data points accepted by the filter
highlight.MicroarrayDataHighlight spots in last plot
hist.MicroarrayDataPlots a histogram
ImaGeneDataThe ImaGeneData class
indexOf.LayoutGets the index of one or more spots from their name or id
isSaturated.MicroarrayDataCheck if some observations are saturated or not
keepSlides.MicroarrayDataRemove all but the specified slides
keepSpots.MicroarrayDataRemove all but the specified spots from all slides
LayoutThe Layout class
LayoutGroupsThe LayoutGroups class
listFlags.MicroarrayDataLists the names of all known flags
loessQuantile.MADataEstimates the (25%,50%,75%) quantile M(A) curves using loess
lowessCurve.MicroarrayDataDraws one or more lowess curves through the data in last plot
MADataThe MAData class
mean.MADataAverage Mean for microarray data
mean.RGDataGenewise Average Mean for channel R and G
MFilterFieldFilter for the log-ratios (M)
MicroarrayDataThe MicroarrayData class
nbrOfColumns.LayoutGets the number of columns on a microarray
nbrOfFields.MicroarrayDataGets the number of fields
nbrOfGrids.LayoutGets the number of grids on a microarray
nbrOfGroups.GeneGroupsGets the number of unique genes
nbrOfRows.LayoutGets the number of rows on a microarray
nbrOfSlides.MicroarrayDataGets the number of slides
nbrOfSlides.SpotPositionGets the number of slides
nbrOfSpots.LayoutGets the size of a microarray
nbrOfSpots.MicroarrayDataGets the number of spots in each of the slides
nbrOfSpots.SpotPositionGets the number of spots in each of the slides
Non-documented_objectsNon-documented objects
normalizeAcrossSlides.MADataNormalizes across slides
normalizeAffine.MADataAffine normalization based on non-logged data
normalizeAffine.RGDataWeighted affine normalization between channels and arrays
normalizeAffineShift.MADataWithin-slide normalization that adjust the channel bias
normalizeCurveFit.MADataWithin-slide normalization that adjust log-ratios by...
normalizeCurveFit.RGDataWithin-slide intensity-dependent normalization in (A,M)
normalizeLogRatioShift.MADataWithin-slide normalization that adjust the log-ratios shift
normalizePlatewise.MicroarrayDataNormalization performed plate by plate
normalizeWithinSlide.MADataWithin-slide normalization
NotFilterThe NotFilter class
OrFilterThe OrFilter class
ParallelFilterThe ParallelFilter class
PlateGroupsThe PlateGroups class
plotDensity.MicroarrayDataPlots the empirical density distribution of a field
plot.MicroarrayDataPlots spatial representation of a microarray spot statistics
plotMvsM.MADataPlots the log-ratios for one slide versus another
plotPrintorder.MicroarrayDataPlots the data as a time series in the order it was printed
plotSpatial3d.MicroarrayDataPlots a 3-dimensional spatial representation of a field
plotSpatial.GenePixDataCreates a spatial plot of a slide
plotSpatial.MicroarrayDataPlots a spatial representation of one field
plotSpatial.QuantArrayDataCreates a spatial plot of a slide
plotSpatial.ScanAlyzeDataCreates a spatial plot of a slide
plotSpatial.SpotDataCreates a spatial plot of a slide
plotSpatial.SpotfinderDataCreates a spatial plot of a slide
plot.SpotPositionPlots the spot positions in an xy scatter plot
plotXY.MicroarrayDataPlots a scatter plot of two fields
points.SpotPositionAdds spot positions to an existing plot
PrintdipGroupsThe PrintdipGroups class
PrinttipGroupsThe PrinttipGroups class
QuantArrayDataThe QuantArrayData class
RawDataThe RawData class
read.ExperimentalSetupReads a file specifying the setup of a microarray experiment
read.GalLayoutReads a GenePix Array List (GAL) file
read.GenePixDataReads one or several GenePix files into one GenePixData...
readHeader.GenePixDataReads a GenePix Results (GPR) file header
read.ImaGeneDataReads an ImaGene result file
read.LayoutReads layout information from a tab-delimited file
read.MicroarrayDataReads microarray data generated by another software package
readOneFile.QuantArrayDataReads a QuantArray result file
readOneFile.SpotfinderDataReads TAV files generated by Spotfinder
read.QuantArrayDataReads one or several QuantArray files into one QuantArrayData...
read.ScanAlyze20DataReads one or several ScanAlyze v2.0 files
read.ScanAlyzeDataReads one or several ScanAlyze files into a ScanAlyzeData...
read.SpotDataReads several Spot files into a SpotData object
read.SpotfinderDataReads several Spotfinder/TAV files into a SpotfinderData...
RejectFilterThe RejectFilter class
removeSlides.MicroarrayDataRemove specified slides
removeSpots.MicroarrayDataRemove specified spots
RGDataThe RGData class
ScanAlyze20DataThe ScanAlyze20Data (ScanAlyze v2.0) class
ScanAlyzeDataThe ScanAlyzeData class
SEFilterFieldFilter for the log-intensities (A)
select.MicroarrayDataSelects rows with certain criteria
SerialFilterThe SerialFilter class
setExtra.MicroarrayDataSets an extra field
setFlag.MicroarrayDataSets the flags on some of the spots
setId.LayoutSets the id of one or more spots
setLabel.MicroarrayDataSets the label of one field
set.LayoutSets the layout
setLayout.MicroarrayDataSets the layout
setName.LayoutSets the name of one or more spots
setParameter.FilterSets the values for a specific parameter for indices accepted...
setProbeWeights.MicroarrayDataSets probe weights on one or several slides
setSaturated.MicroarrayDataSet which observations in a given channel that are saturated...
setSlideNames.MicroarrayDataSets the names of the slides
setVisible.FilterSets if the filter should bee visible or not
shift.MADataShift the log-ratios, log-intensities or the raw signal
shift.RawDataShift the log-ratios, log-intensities or the raw signal
shift.RGDataShift the log-ratios, log-intensities or the raw signal
size.LayoutGets the size of a microarray
size.MicroarrayDataGets the number of spots in all slides together
size.SpotPositionGets the number of spots in all slides together
SlideColumnGroupsThe SlideColumnGroups class
SlideRowGroupsThe SlideRowGroups class
SMAThe SMA class
SpotDataThe SpotData class
SpotfinderDataThe SpotfinderData class
SpotPositionClass representing spot positions
str.MicroarrayDataCompactly Display the Structure of a MicroarrayData object
subplots.MicroarrayDataPrepare for a grid of subplots based on the number of slides
summary.MicroarrayDataGets summary statistics for the fields
swapDyes.MADataDye swap one or many slides
swapDyes.RawDataDye swap one or many slides
swapDyes.RGDataSwap dyes of one or many slides
text.FilterLabels the data points accepted by the filter
text.MicroarrayDataPuts labels to the spots in last plot
toPrintorderMatrix.LayoutGets a matrix of spot indices in the order they were printed
topSpots.MADataGets the top spots
toXYMatrix.LayoutLayouts out values in the same way as the spots are layout
unite.MicroarrayWeightsCoalesce weights of lower order into higher order weights
validateArgumentChannels.GenePixDataValidates the argument 'channels'
validateArgumentGroupBy.MicroarrayDataValidates the argument 'groupBy'
validateArgumentSlide.MicroarrayDataValidates the argument 'slide'
validateArgumentSlides.MicroarrayDataValidates the argument 'slides'
validateArgumentWeights.MicroarrayDataValidates the argument 'weights'
var.MADataVariance for microarray data
var.RGDataGenewise Variance for channel R and G
WeightsWeights
write.GenePixDataWrite a GenePix Results Data file
write.ImaGeneDataWrite an ImaGene result data file
write.LayoutWrites the layout information to a tab-delimited file
write.MicroarrayDataWrite a MicroarrayData object to file
write.QuantArrayDataWrite a QuantArray result data file
write.ScanAlyze20DataWrites a ScanAlyze v2.0 Results Data file (NOT IMPLEMENTED)
write.ScanAlyzeDataWrite a ScanAlyze Results Data file
write.SpotDataWrite a SpotData object to file
write.SpotfinderDataWrite a SpotfinderData object to file
write.SpotPositionWrite a SpotPosition object to file
HenrikBengtsson/aroma documentation built on May 8, 2017, 3:58 p.m.