Man pages for GRIN2
Genomic Random Interval (GRIN)
| alex.boxplots | Generate Box Plots of Gene Expression by Lesion Groups |
| alex.pathway | Visualize Lesion and Expression Data by Pathway |
| alex.prep.lsn.expr | Prepare Lesion and Expression Data for Kruskal-Wallis Test |
| alex.waterfall.plot | Generate Waterfall Plot of Lesion and Expression Data |
| alex.waterfall.prep | Prepare Lesion and Expression Data for Waterfall Plots |
| clin_data | Example Clinical Dataset for T-cell Acute Lymphoblastic... |
| compute.gw.coordinates | Compute Genome-wide Plotting Coordinates |
| count.hits | Count Gene-Lesion Hits |
| default.grin.colors | Assign Default GRIN Colors |
| example_exon_annotation | Example Human Exon Annotation Data |
| expr_data | Example T-ALL Gene Expression Dataset |
| find.gene.lsn.overlaps | Find Gene-Lesion Overlaps |
| genomewide.log10q.plot | Genome-wide -log10(q-value) Plot |
| genomewide.lsn.plot | Genome-wide Lesion Plot |
| get.chrom.length | Get Chromosome Length |
| get.ensembl.annotation | Retrieve Ensembl Annotation Data |
| grin.assoc.expr.outcome | Association Between Gene Expression and Clinical Outcomes |
| grin.assoc.lsn.outcome | Associate Binary Genomic Lesions with Clinical Outcomes |
| grin.barplt | GRIN Lesion Stacked Bar Plot |
| grin.logRank | Log-Rank Test for Associations Between Genomic Lesions and... |
| grin.lsn.boundaries | GRIN Evaluation of Lesion Boundaries |
| grin.oncoprint.mtx | GRIN OncoPrint-Compatible Lesion Matrix |
| grin.results | Example GRIN2 Analysis Results |
| grin.stats | Execute the GRIN Statistical Framework |
| grin.stats.lsn.plot | GRIN Lesion and Statistics Plot |
| hg38_chrom_size | Chromosome Length Data (GRCh38) |
| hg38_cytoband | GRCh38 Chromosome Cytobands |
| hg38_exon_chrom_size | Human GRCh38 Chromosome-Level Exon Target Sizes |
| hg38_gene_annotation | Example Gene Annotation Data |
| KW.hit.express | Associate Lesion Groups with Gene Expression |
| lesion_data | Example T-ALL Lesion Dataset |
| lsn.transcripts.plot | Plot Genomic Lesions with Transcript Annotations |
| onco.print.props | Oncoprint Proportions by Lesion Type |
| order.index.gene.data | Order and Index Gene Annotation Data |
| order.index.lsn.data | Order and Index Lesion Data |
| pathways | Genes Annotated to Biological Pathways |
| prep.binary.lsn.mtx | Prepare Binary Lesion Matrix |
| prep.gene.lsn.data | Prepare Gene and Lesion Data for GRIN Analysis |
| prep.lsn.type.matrix | Prepare Lesion Type Matrix |
| prob.hits | Find Probability of Locus Hit |
| top.alex.waterfall.plots | Generate Waterfall Plots for Significant Genes |
| write.grin.xlsx | Write GRIN Results to an Excel File |
