Man pages for elqumsan/RNAseqMVA
Application of Multivariate Analysis methods to RNA-seq Data

buildAttributesbuild attributes for an object depending on its class
buildAttributes.DataTableWithClassesbuild the attributes of an object of class...
buildAttributes.DataTableWithTrainTestSetsbuild the attributes that depend on the count table
buildAttributes.defaultdefault method to build attributes for an object.
DataTableWithClassesconstructor of the DataTableWithClasses class
DataTableWithTrainTestSetsRandom sampling of n training sets in a DataTableWithClasses.
DEGorderingVariable ordering according to the p-values returned by...
ErrorRateBoxPlotFunction for boxplot the error rate
exportTablesExport the different fields of an object in tab-separated...
exportTables.DataTableWithClassesExport the different fields of an object of class...
exportTables.DataTableWithTrainTestSetsExport the tables specific to the class...
exportTables.defaultdefault export table (for closing the NextMethod calls)
exportTables.StudyCaseExport the tables specific to the class StudyCase
ExtractPhenoTableFuction for extracting Pheno Table from specified recount...
filterDataTableApply various filters on the observations and variables of a...
geocharFromPhenoExtract the conditions from the "characteristics" column of...
heatmap.TrainTestResultheat map is a fales color image with pattern added to the...
helloHello, World!
histCountsPerGeneClassDraw an histogram with the raw counts per gene
histCountsPerGeneClass.StudyCaseDraw an histogram with the raw counts per gene
initParallelComputinginitialise parameters for parallel computing with foreach and...
initRecountIDIntialise parameters and directories for a give recount ID.
IterateTrainingTestingIterate training/testing procedures with a given classifier...
IterateTrainingTesting.DataTableWithClassesIterate training/testing procedures with a given classifier...
IterateTrainingTesting.DataTableWithTrainTestSetsIterate training/testing procedures with a given classifier...
IterateTrainingTesting.defaultprinting report message to informaing so, Iterate...
LibsizeBarplotDraw a barplot with the number of million reads per sample
LibsizeRankPlotRank plot of RNA-seq library sizes
loadCountsLoading the count table, the Pheno table and vector of class...
loadMemoryImageLoad a previous analysis previously stored as memoy image
loadRecountExperimentLoading one count table from Recount repository by given...
LoadRequiredBioconductorPackagesLoad required packages from BioConductor, afte having...
LoadRequiredCRANPackagesLoad required packages from CRAN, after having installed them...
MergeRunsMerge read counts from different runs by sample.
message.with.timeprint a message preceded by currrent tume
MisclassificationEstimateRNA-Seq classifier evaluation to assesse the performance of...
NormalizeSamplesscaling RNA-seq count table
outputParametersreturn output parameters (output directory, file prefix,...
plot2PCsPlot two components of prcomp transform
plotFiguresplot diagnostic figures for specific classes of objects
plotFigures.DataTableWithClassesplot diagnostic figures for an object of the class...
plotFilterHistogramsplot histograms of the variance distributions at different...
print.DataTableWithClassesfinish summary of an object belonging to class...
print.DataTableWithTrainTestSetsprint of an object belonging to class...
print.StudyCaseprint a summary of an object belonging to class StudyCase
print.TrainTestResultprinting the attribute of object that had TraiTestResult...
RunDESeq2run DESeq2 to test differential expression on each feature of...
RunDESeq2.StudyCaserun DESeq2 on an object of class StudyCase
RunedgeRrun edgeR to test differential expression on each feature of...
RunedgeR.StudyCaserun edgeR on an object of class StudyCase
RunViRfrun variable importance by random Forest to on an object of...
RunViRf.StudyCaserun variable importance by random Forest on an object of...
saveMemoryImageSave a memory image in order to be able to reload all results...
selectProjectsByCharacteristicsSelect Recount projects based on the presence of...
StudyCaseCreate a StudyCase object, load RecountID dataset, and...
SummarizeErrorTablegenerate a summary table from a list of error table files.
summary.DataTableWithClassesprint a summary of an object belonging to class...
summary.DataTableWithTrainTestSetsprint a summary of an object belonging to class...
summary.defaultfinish summary of an object belonging to class...
summary.StudyCaseprint a summary of an object belonging to class StudyCase
TrainTestResultClass to handle the results of Training-Testing evaluation...
XYplotDraw an XY plot to compare the mean counts per gene for two...
elqumsan/RNAseqMVA documentation built on Sept. 26, 2018, 4:57 a.m.