Man pages for jefferys/fusionExpressionPlot
Plot Expression Profiles for Fused Genes

addExonExpressionAdd exon expression file data to an existing data frame
do.allPlotsGenerate fusion expression plots
do.plotsPlot fusion gene expression
extractGeneModelsExtract gene models from the GAF
extractTranscriptModelsExtract transcript models from the GAF
filterFusionsSub-select fusion lines from a list of fusions
FusionExpressionPlotPlot Expression Profiles for Fused Genes
genomicToModelCoordinatesConvert from genomic feature to model coordinates.
getCandidateFusionsSelect candidate fusions by sample and gene
getCohortExonExpressionDataGenerate a data frame of cohort exon expression data
getFusionExpressionPlotDataGenerate the plot data object for a fusion expression plot.
getMapSpliceCohortFusionDataLoad a mapplice cohort fusion file.
grAddColumnAdd a data column to a GRanges object.
grFromCohortDfExtract GRange objects from cohort exon expression data
grFromElementStringConvert a genomic element string into an GRanges object.
grFromLocationStringConvert a genomic location string into a GRange object.
grNewCreate a simple GRanges object.
grToElementStringExtract a genomic element string from a GRange object
grToLocationStringExtract a genomic location string from a GRange object
grToRectPlotable rectangles from GRanges Object
is.safeFileNameVerify that a fileName is safe for use in shell commands.
loadCohortDefinitionRead in the cohort definition file
loadExonExpressionFileLoad a TCGA exon expression data file as a data frame
loadGafModelsLoad a GAF models file into a per exon data frame.
mapColorsMap colors to values
mapLabelsMaps values into labeled bins
normExpressionDataNormalize a cohort of exon expression data
plotFusionExpressionOnePlot a one-gene fusion expression plot.
plotFusionExpressionPairPlot a two-gene fusion expression plot.
plotFusionExpressionPlotDataPlot a fusionExpressionPlotData object
plotGeneExpressionPlot the expression of a gene
pointToPolyConvert points to polygons
regexprNamedMatchesExtract matched named substrings
slurpRead a file's lines in as vector
templateFillEvaluate and fill string templates
jefferys/fusionExpressionPlot documentation built on May 19, 2019, 3:59 a.m.