Man pages for bedapub/ribiosExpression
Expression analysis component of ribios

annotateAnnotate eSet or probesets
annotate-character-character-logical-methodAnnotate probesets with a chip type
annotate-character-character-missing-methodAnnotate probesets with a chip type without checking
annotate-eSet-character-logical-methodAnnotate an eSet object with a chip type
annotate-eSet-character-missing-methodAnnotate an eSet object with a chip type, do not perform...
assertFullRankAssert whether a matrix is of full rank numerically
ChipFetcher2ExpressionSetImport ChipFetcher export files into an ExpressionSet object.
contrastMatrixExtract the contrast matrix from an object
contrastNamesExtract contrastNames from an object
contrastSampleIndicesReturn indices of samples involved in the given contrast of...
dataFrameTwoVecsBuild a data.frame from two vectors of potential different...
design2groupInfer groups from a design matrix
DesignContrastContrast a DesignContrast object
DesignContrast-classStudy design and contrast information
designMatrixExtract the design matrix from an object
designVariablesExtract design variable names from an object
dispGroupsExtract displayed group labels from an object
eSetToLongTableTransform eSet to long data.frame
exprsToLongTransform an expression matrix to long table
fixEmptyColumnNameDetect if any column has an empty string as name and fix
formatGmtMake strings in the GMT format
groupsExtract sample groups from an object
grp2gmtConvert GRP files into GMT-formatted strings
isInputDesignConsistentTest whether the input design matrix is consistent with the...
keepMaxStatProbeFilter multiple probesets matching to the same gene by...
limmaTopTable2dgeTableTransform limma::topTable results to a DGEtable
matrixToLongTableTransform a matrix to long table
mergeEsetMerge two eSets by column binding
nContrastExtract the number of contrasts from an object
parseContrastStrParse contrast from strings
parseDesignContrastParse study design and asked questions encoded in design and...
parseDesignContrastFileParse design and contrast from files
parseDesignContrastStrParse design and contrast from strings
readAnnotationFileRead in an annotation file in the tsv-format, with or without...
readEsetRead eSet object from plain files
readExprsMatrixRead an expression matrix into an ExpressionSet object
readFeatureAnnotationFileRead in feature annotation file in the tsv-format, with or...
readFKtableRead table with Foreign Keys
readGctClsImport ExpressionSet into gct/cls files the C version, about...
readSampleAnnotationFileRead in sample annotation file in the tsv-format, with or...
reannotateTransform an eSet object of Bioc-annotation into of...
removeColRankReturn rank of the matrix and the ranks of resulting matrices...
ribiosExpression-packageData structures and functions for gene expression analysis
ribios.ExpressionSetAn ExpressionSet for case demonstrations
rowscale.ExpressionSetPerform row-wise scaling to an ExpressionSet object
sniffFeatureTypeSniff the feature type of an object that implements the...
splitPCASplit an eSet object and run PCA on each split, return PCA...
summarizeProbesetsSummarize probesets belonging to the same gene
summarizeSamplesSummarize samples by applying the function to sample subsets
truncateDgeTableTruncate dgeTable into tables of positively and negatively...
writeEsetExport an ExpressionSet object as tab-delimited (or gct)...
writeGctExport matrix or eEset that can be coereced as one into...
writeGctClsExport ExpressionSet as Gct/Cls files
writeSampleGroupsWrite sample groups and group levels into plain text files
bedapub/ribiosExpression documentation built on July 22, 2020, 4:07 p.m.