Man pages for GRIN2
Genomic Random Interval (GRIN)
| alex.boxplots | Prepare Box Plots of Expression Data by Lesion Groups |
| alex.pathway | Associate Lesions with Expression Data on the Pathway Level |
| alex.prep.lsn.expr | Prepare Lesion and Expression Data for Kruskal-Wallis Test |
| alex.waterfall.plot | Prepare Waterfall Plot of Lesion and Expression Data |
| alex.waterfall.prep | Prepare Lesion and Expression Data for Waterfall Plots |
| clin.data | Example T-ALL Dataset Clinical Data |
| compute.gw.coordinates | Compute Genome-wide Coordinates |
| count.hits | Count Gene Lesion Hits |
| default.grin.colors | Default GRIN Colors |
| expr.data | Example T-ALL Dataset Gene Expression Data |
| find.gene.lsn.overlaps | Find Gene Lesion Overlaps |
| genomewide.log10q.plot | Genomewide log10q Plot |
| genomewide.lsn.plot | Genome-wide Lesion Plot |
| get.chrom.length | Get Chromosome Length |
| get.ensembl.annotation | Get Ensembl Gene and Regulatory Features Annotation Data |
| grin.assoc.lsn.outcome | Associate Lesions with Clinical Outcomes |
| grin.barplt | GRIN Bar Plot |
| grin.lsn.boundaries | GRIN Evaluate Lesion Boundaries |
| grin.oncoprint.mtx | GRIN OncoPrint Matrix |
| grin.stats | GRIN Statistics Output |
| grin.stats.lsn.plot | GRIN Statistics Lesions Plot |
| hg19.chrom.size | Chromosome Length Data File |
| hg19_cytoband | GRCh37 Chromosome Cytobands |
| hg19.gene.annotation | Example Gene Annotation Data File |
| hg38_cytoband | GRCh38 Chromosome Cytobands |
| KW.hit.express | Associate Lesion with Expression Data Using Kruskal-Wallis... |
| lesion.data | Example T-ALL Dataset Lesion Data |
| lsn.transcripts.plot | Lesions Gene Transcripts Plot |
| onco.print.props | Oncoprint proportions |
| order.index.gene.data | Order Index Gene Data |
| order.index.lsn.data | Order Index Lesion Data |
| pathways | List of Genes Annotated to a Group of Pathways |
| prep.binary.lsn.mtx | Prepare Binary Lesion Matrix |
| prep.gene.lsn.data | Prepare Gene and Lesion Data |
| prep.lsn.type.matrix | Prepare Lesion Type Matrix |
| prob.hits | Find Probablity of Locus Hit |
| top.alex.waterfall.plots | Waterfall Plots for Lesion and Expression Data of Top... |
| write.grin.xlsx | Write GRIN Results |
