Man pages for jefferys/fusionExpressionPlot
Plot Expression Profiles for Fused Genes
| addExonExpression | Add exon expression file data to an existing data frame |
| do.allPlots | Generate fusion expression plots |
| do.plots | Plot fusion gene expression |
| extractGeneModels | Extract gene models from the GAF |
| extractTranscriptModels | Extract transcript models from the GAF |
| filterFusions | Sub-select fusion lines from a list of fusions |
| FusionExpressionPlot | Plot Expression Profiles for Fused Genes |
| genomicToModelCoordinates | Convert from genomic feature to model coordinates. |
| getCandidateFusions | Select candidate fusions by sample and gene |
| getCohortExonExpressionData | Generate a data frame of cohort exon expression data |
| getFusionExpressionPlotData | Generate the plot data object for a fusion expression plot. |
| getMapSpliceCohortFusionData | Load a mapplice cohort fusion file. |
| grAddColumn | Add a data column to a GRanges object. |
| grFromCohortDf | Extract GRange objects from cohort exon expression data |
| grFromElementString | Convert a genomic element string into an GRanges object. |
| grFromLocationString | Convert a genomic location string into a GRange object. |
| grNew | Create a simple GRanges object. |
| grToElementString | Extract a genomic element string from a GRange object |
| grToLocationString | Extract a genomic location string from a GRange object |
| grToRect | Plotable rectangles from GRanges Object |
| is.safeFileName | Verify that a fileName is safe for use in shell commands. |
| loadCohortDefinition | Read in the cohort definition file |
| loadExonExpressionFile | Load a TCGA exon expression data file as a data frame |
| loadGafModels | Load a GAF models file into a per exon data frame. |
| mapColors | Map colors to values |
| mapLabels | Maps values into labeled bins |
| normExpressionData | Normalize a cohort of exon expression data |
| plotFusionExpressionOne | Plot a one-gene fusion expression plot. |
| plotFusionExpressionPair | Plot a two-gene fusion expression plot. |
| plotFusionExpressionPlotData | Plot a fusionExpressionPlotData object |
| plotGeneExpression | Plot the expression of a gene |
| pointToPoly | Convert points to polygons |
| regexprNamedMatches | Extract matched named substrings |
| slurp | Read a file's lines in as vector |
| templateFill | Evaluate and fill string templates |
