Man pages for asishallab/GeneFamilies
Analyses different properties of gene families

addAlphaAdds an alpha value to colors.
addGeneIdsCols2HomologsKaKsTableExtracts the gene pairs' identifiers from the 'Sequence'...
addGeneIdsCols2OrthologsKaKsTableUses 'gene.1' as the first member of the orthologous gene...
alignAAStringSetAligns the set of amino acid sequences based on the chemical...
alignCDSSetWithAlignedAAsAsGuideUses an amino acid multiple sequence alignment to guide the...
alignCDSWithAlignedAASeqUses an amino acid multiple sequence alignment to guide the...
alignCodingSequencesPipelineRuns the pipeline to align a set of coding sequences: First...
annotationBasedShannonEntropyCompute Shannon Entropy ('entropy') as a measure of...
annotationEvolutionMeasures annotations gained, lost, and shared between base...
annotationMatrixGenerate a 2x2 contingency table for statistical hypothesis...
appendToTestedHypothesesFunction appends a row to the argument data.frame 'df', which...
axtExtracts pairs of genes from a CDS multiple sequence...
buildPhylogeneticTreeUses FastTree[MP] to generate a maximum likelihood tree based...
cbindAnnotationDescriptionAdds a column to 'enrichment.tbl' holding human readable...
classSpecificExpressionProfileDistsComputes the within 'stats' of expression profile distances...
closestHomologUses pairwise sequence similarity search results in order to...
codeml.tmplTemplate for brew to generate the control file used as input...
collectNonConservedAnnotationsFor each species identifies those annotations that are non...
compositeAnnotationsGenerates a list of composite Annotations found for the...
computeKsPipelineRuns the pipeline to compute the Ks values of gene pair 'x'...
computeOrthologSpecificAnnotationDiversityPerGroupWrapper for function...
computeSpeciesSpecificAnnotationDiversityPerGroupComputes the annotation (function) based Shannon Entropy per...
conservedOrthologsIdentifies those pairs of orthologous genes where one member...
constructAnnotationVectorSpaceFor the argument 'genes' construct a vector space based on...
correlationRpkmCopyNoGenerates a data.frame of the Genes' names, copy numbers, and...
cosAngleVecComputes the cosine of the angle between the two...
cosDiagCompute cosinus of the angle between argument vector 'x' and...
distNormExprVectrsReturns the vector resulting from subtracting 'e.v.b' from...
distVectorCloudsMeasures the distance between two vector clouds (see...
domainsForPosLooks up the conserved protein domains (InterPro) that have...
enrichedAnnotationsTests the NULL Hypothesis for each gene (function) annotation...
enrichmentTestsTests for every function annotation in 'case.anno.tbl' the...
euclNormComputes the Euclidean norm (length) of vector 'x'.
expressionProfileDistStatsPerTissuesExtract different 'stats' per tissue specific expression...
expressionProfilesDistsComputes the distance ('base::dist') between the expression...
exprVecSpaceEvolutionAfterDuplBased on an expression vector space infers the evolution of...
extractFamilyNameGiven a character vector regular expressions are applied to...
familyExpandedAlternative method to detect expanded or compressed families...
foregroundNodesIdentifies those tip and inner nodes of the phylogenetic tree...
formatNodeLabelsFor a default phylogentic tree this formats the local support...
geneClassesVectorCloudsInvokes 'GeneFamilies::statVectorCloud' on each subset of...
geneGroupsAnnotationBasedShannonEntropyComputes for each gene group in 'groups.ids' the annotation...
geneGroupSubfunctionalizationInvokes 'subfunctionalizationAnnotationBased' for all...
genePairInRedisChecks wether in the current Redis server there is an entry...
generateContingencyTableGenerates a matrix that can directly be used as input for...
getFamilyDNAStringSetExtracts the coding sequences of the gene members of the...
getMcCoresReads out SHELL environment variable 'MCCORES' and returns it...
getSpeciesNodeNumberFromCafeExtracts the number CAFE assigned the species during its...
goEnrichTestComputes a Gene Ontology (GO) enrichment test using the...
hasInvalidVecSpaceComponentsGeneric function to check wether any vector component is...
hasInvalidVecSpaceComponents.data.frameGeneric function to check wether any vector component is...
hasInvalidVecSpaceComponents.matrixGeneric function to check wether any vector component is...
hasInvalidVecSpaceComponents.numericGeneric function to check wether any vector component is...
homologsIdentify homologous gene pairs in a table of significantly...
hyphy.branch.site.bfBrew template to generate a family's BranchREL input file
hyphy.busted.bfBrew template to generate a family's BUSTED input file
hyphy.fubar.bfBrew template to generate a family's FUBAR input file
hyphy.meme.bfBrew template to generate a family's MEME input file
inferExpectedFalsePositiveRateTranslates the FUBAR reported expected absolute NUMBER of...
interVsIntraSpeciesExpressionProfileDistsExtracts the inter- and intra-species distances from argument...
iprWithSelectedAAIdentifies conserved protein domains (InterPro) overlapping...
joinGOEnrichResultsMethod extracts all GO ontology specific enrichment result...
loadDnaFastaSimple wrapper around seqinr::read.fasta for DNA data....
matchingSpliceVariantAssuming 'gene.ids' holds gene identifiers that lack splice...
maxMinusMinComputes the absolute distance between maximum and minimum,...
maxValuesFromInterVsIntraSpeciesExpressionProfileDistsGenerates a data.frame with one row for each family with...
mclDataFrameAsListConverts the data.frame of gene families into a list of gene...
mr.bayes.cds.treeBrew template to generate an Mr Bayes input file for a...
mrBayesCdsTreeGenerates a valid input file for Mr Bayes, which will...
mr.bayes.mixed.cds.treeBrew template to generate a coding sequences group's Mr Bayes...
mr.bayes.mixed.prot.treeBrew template to generate a protein group's Mr Bayes input...
mrBayesProteinTreeGenerates a valid input file for Mr Bayes, which will...
mrBayesProteinTreeFromMixedMSAGenerates a valid input file for Mr Bayes, which will...
mr.bayes.prot.treeBrew template to generate a protein group's Mr Bayes input...
mrBayesTreeFromMixedMSAGenerates a valid input file for Mr Bayes, which will...
naAsZeroHelper function that converts argument 'x' to the number zero...
nonConservedAnnotationsIdentifies those gene annotations that are non conserved...
nonConservedCompositeAnnotationsIdentifies those composite annotations that are less frequent...
normalizeVectorNormalizes the vector 'x' to length 1.0.
numberAnnotationsCounts the number of times an annotation, e.g. a Pfam or...
orthologsIdentifies orthologous gene pairs as genes being...
orthologsFromBLATpslTableParses 'psl' default BLAT output formatted files to infer...
parseCafeBranchSpecificPValuesExtract the branch specific extension / contraction P-Values...
parseMemeBranchResultsParses a HyPhy MEME branch result file to extract significant...
passSupportValuesPasses support values from inner nodes in argument 'trees' to...
perpVecToDiagonalDrops a perpendicular from vector 'x' to the vector space's...
plotSpeciesSpecificAnnotationDiversityScatter-Plots the pecies specific annotation (function)...
plotSpeciesSpecificAnnotationDiversityDistsBoxplots the distributions of species specific annotation...
plotTissueSpecificExpressionProfileDistanceDistribsPlots horizontal boxplots of per tissue distributions of...
procGOHyperGResultConverts an instance of GOHyperGResult into a table...
putGenePairIntoRedisPuts the integer value 1 into the Redis Server using the...
rad2degConverts an angle's size given in 'radians' to 'degrees'.
readBlatPSLoutputWraps function base::read.table with the proper arguments...
readFubarTableParses a FUBAR output table for significant posterior...
readInterProScanResultTableParses the result file of InterProScan into a data.frame.
readKaKsCalculatorOutputUses base::read.table to parse the output of...
readMclOutputUses Linux's AWK and package data.table to parse the output...
readMinimumInterProScanResultTableUses function...
removeDuplicatedInversePairsIdentifies duplicated inverse pairs and discards them.
removeExpressionVariantModifies the argument 'gene.ids' by deleting expression...
removeNodeLabelsAndBranchLengthsRemoves node labels and branch lengths from instance of...
removeSpliceVariantRemoves trailing splice variant identifier from gene IDs;...
renderCodemlInputsGenerates the tree and control file to run PAML's codeml in...
replaceSanitizedWithOriginalIDsReplaces sanitized protein identifiers in XStringSet...
replaceWithOriginalReturns the matching original names for the sanitized ones...
replaceWithOriginalInFigTreeUses GNU sed to replace the sanitized gene identifiers with...
sanitizeNamesMany programs in Bioinformatics cannot handle gene accessions...
scalarProjectionComputes the scalar projection of vector 'a' onto vector 'b',...
selectGeneGroupSpecificEnrichedAnnotationsInfer enriched annotations specific to the argument type of...
selectSignificantEnrichmentsFilters 'enrichment.tbl' for those annotations that have a...
selectSignificantlyEnrichedAnnotationsSelects those results obtained from calling...
shannonEntropyComputes the normalized empirical Shannon Entropy for counts...
speciesCompositionInfers the number of genes belonging to the given species.
speciesCompositionsToDataFrameGenerate a data frame of the list of species composition...
speciesForGeneIdIdentifies the species of a gene identifier using the...
speciesForGeneId_RegexIdentifies the species of a gene identifier using regular...
spec.regex.gene.ids#################### Define constants: # ####################...
statVectorCloudComputes the statistic 'stat' (default is 'base::mean')...
subfunctionalizationAnnotationBasedIdentifies instances of subfunctionalization occurred in the...
subTreesIdentifies a list of sub-trees in argument tree initiating...
testAnnotationBasedSpeciesSpecificNeofunctionalizationStatistically tests the NULL Hypotheses that the annotation...
testExprVecSpaceEvolutionAfterDuplTesting function 'exprVecSpaceEvolutionAfterDupl'.
testHomologsTest of function 'homologs(...)'
testHourglassModelTest the hypothesis of the developmental hourglass by...
testNonConservedAnnotationsTest function 'nonConservedAnnotations'
testNonConservedCompositeAnnotationsTest for function nonConservedCompositeAnnotations.
testShannonEntropyTesting function 'GeneFamilies::shannonEntropy'
testSubfunctionalizationAnnotationBasedTesting 'subfunctionalizationAnnotationBased'
transcriptsPerKilobaseMillionCalculates Reads Per Kilobase Million (RPKM) RPKM = (Rg *...
translate2AASeqsUses the program MACSE to translate the coding sequences to...
tree4BustedAnnotates a phylogenetic tree in such amanner that foreground...
unalignedAAforAlignedAAPosComputes the position in the unaligned sequence of a...
upperWhiskerIdentifies the value that corresponds to the upper whisker...
validateAASeqsValidates an AAString
validateAAStringSetValidates an AAStringSet
vectorProjectionComputes the vector projection of vector 'a' onto vector 'b',...
writeAxtWrites pairwise aligned sequences to a file of AXT format for...
asishallab/GeneFamilies documentation built on Oct. 5, 2018, 7:26 p.m.